[Cluster classification and clinical prognostic modeling based on m6A RNA methylation regulators in liver cancer]

Objective: Cluster classification based on m6A methylation regulators and construct prognostic evaluation model. Methods: Utilizing consensus cluster to classify the liver cancer samples form TCGA based on the expression of 13 m6A methylation regulators, and verify the function and prognostic significance of the clustered subtypes. Marker genes were further screened to construct a risk prediction model for evaluating the prognosis of liver cancer patients. Results: The two clustered subtypes based on m6A methylation regulators showed significant differences in the prognosis value of liver cancer patients (P=0.048), and 38 prognostic markers related to m6A methylation in liver cancer were screened from the subgroup with poor prognosis. Two m6A regulatory genes, YTHDF1 and YTHDF2, are proved with adverse prognosis by univariate cox analysis (P<0.05, Hazard ratio>1). We used Lasso regression method to build risk assessment model and effectively predicted the prognosis status of liver cancer patients within 4 years (4-year AUC=0.685, 3-year AUC=0.669). Moreover, the assessment model was validated in another dataset of Asia liver cancer patients. Conclusion: The study provided ideas for studying m6A methylation in liver cancer, and the risk prediction model can be used to evaluate the short-term prognosis of liver cancer patients.

Planctomonas psychrotolerans sp. nov., isolated from rhizosphere soil of Suaeda salsa

A psychrotolerant actinobacterium, designated strain J5903^T, was isolated from an alkaline soil sample from the rhizosphere of Suaeda salsa collected in desertification land surrounding Jiuliancheng Nur in Hebei Province, PR China. Cells of the isolate were Gram-stain-positive, aerobic, non-motile and non-spore-forming cocci. Strain J5903^T grew optimally at 20‒25 °C, at pH 7.0‒7.5 and with <1 % (w/v) NaCl. The cell-wall peptidoglycan type was B2γ with d-2,4-diaminobutyric acid and l-2,4-diaminobutyric acid as diagnostic amino acids. The muramyl residue was acetyl type. The menaquinones were MK-11, MK-12, MK-10 and MK-13. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid. The major whole-cell fatty acids were anteiso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The genomic DNA G+C content was 69.1 mol%. It shared the highest average nucleotide identity and digital DNA-DNA hybridization values with Planctomonas deserti 13S1-3^T. Phylogenies based on genome sequence showed that strain J5903^T and P. deserti 13S1-3^T formed a robust cluster with high bootstrap support. Strain J5903^T shared typical chemotaxonomic characteristics with P. deserti 13S1-3^T. Combining the polyphasic taxonomic evidence, strain J5903^T represents a novel species of the genus Planctomonas, for which the name Planctomonas psychrotolerans sp. nov. is proposed. The type strain is J5903^T (=DSM 101894^T=CGMCC 1.15523^T).

Phytoactinopolyspora mesophila sp. nov., isolated from a saline-alkaline soil

A novel moderately halophilic, filamentous actinobacterium, designated as XMNu-373^T, was isolated from a saline-alkaline soil sample collected from the Mongolia Plateau, Dongwu County, Inner Mongolia Autonomous Region, PR China. The isolate grew optimally at 28‒37 °C, pH 7.0‒8.0 and with 2-5 % (w/v) NaCl. The substrate mycelia fragmented into rod-like elements, and the white aerial mycelia formed spore chains at maturity. The predominant menaquinone was MK-9(H₄). The polar lipids were diphosphatidylglycerol, three unidentified phosphoglycolipids, an unidentified aminophospholipid, two phosphatidylinositol mannosides, four unidentified phospholipids, phosphatidylglycerol and two unidentified lipids. The major cellular fatty acids were iso-C_16 : 0, anteiso-C_17 : 0 and anteiso-C_15 : 0. The genomic DNA G+C content was 66.2 mol%. It shared high 16S rRNA gene sequence similarities to Phytoactinopolyspora halotolerans YIM 96448^T (96.1 %) and Phytoactinopolyspora endophytica EGI 60009^T (96.0 %). Phylogenetic trees based on 16S rRNA gene sequences revealed that strain XMNu-373^T resided in the clade of family Jiangellaceae, and it formed a monophyletic branch distinct from four other recognized type species in the subclade of the genus Phytoactinopolyspora. On the basis of polyphasic taxonomic evidence, strain XMNu-373^T represents a novel species of the genus Phytoactinopolyspora, for which the name Phytoactinopolyspora mesophila sp. nov. is proposed. The type strain is XMNu-373^T (=JCM 33740^T=CGMCC 4.7654^T).

Mutation analysis of FBN1 gene in two Chinese families with congenital ectopia lentis in northern China

AIM

To summarize the phenotypes and identify the underlying genetic cause of the fibrillin-1 (FBN1) gene responsible for congenital ectopia lentis (EL) in two Chinese families in northern China.

METHODS

A detailed family history and clinical data from all participants were collected by clinical examination. The candidate genes were captured and sequenced by targeted next-generation sequencing, and the results were confirmed by Sanger sequencing. Haplotyping was used to confirm the mutation sequence. Real-time PCR was used to determine the FBN1 messenger ribonucleic acid (mRNA) levels in patients with EL and in unaffected family members.

RESULTS

The probands and other patients in the two families were affected with congenital isolated EL. A heterozygous FBN1 mutation in exon 21 (c.2420_IVS20-8 delTCTGAAACAinsCGAAAG) was identified in FAMILY-1. A heterozygous FBN1 mutation in exon 14 (c.1633C>T, p.R545C) was identified in FAMILY-2. Each mutation co-segregated with the affected individuals in the family and did not exist in unaffected family members and 200 unrelated normal controls.

CONCLUSION

The insertion-deletion mutation (c.2420 IVS20-8delTCTGAAACA insCGAAAG) in the FBN1 gene is first identified in isolated EL. The mutation (c.1633C>T) in the FBN1 gene was a known mutation in EL patient. The variable phenotypes among the patients expand the phenotypic spectrum of EL in a different ethnic background.

Blockade of the forward Na+ /Ca2+ exchanger suppresses the growth of glioblastoma cells through Ca2+ -mediated cell death

Background and Purpose

The Na⁺/Ca²⁺ exchanger (NCX) working in either forward or reverse mode participates in maintaining intracellular Ca²⁺ ([Ca²⁺]_i) homeostasis, which is essential for determining cell fate. Previously, numerous blockers targeting reverse or forward NCX have been developed and studied in ischaemic tissue injury but barely examined in glioblastoma for the purpose of anti‐tumour therapy. We assessed the effect of NCX blockers on glioblastoma growth and whether NCX can become a therapeutic target.

Experimental Approach

Patch‐clamp recording, Ca²⁺ imaging, flow cytometry, and Western blot were used to study the effects of specific and non‐specific NCX blockers on cultured glioblastoma cells. In vivo bioluminescent imaging was used to measure effects on grafted glioblastoma.

Key Results

Selectively blocking the reverse NCX with SEA0400, SN‐6, and YM‐244769 did not affect tumour cell viability. Blocking the forward NCX with bepridil, CB‐DMB, or KB‐R7943 elevated [Ca²⁺]_i and killed glioblastoma cells. Bepridil and CB‐DMB caused Ca²⁺‐dependent cell cycle arrest together with apoptosis, which were all attenuated by a Ca²⁺ chelator BAPTA‐AM. Systemic administration of bepridil inhibited growth of brain‐grafted glioblastoma. Bepridil did not appear to have a cytotoxic effect on human astrocytes, which have higher functional expression of NCX than glioblastoma cells.

Conclusions and Implications

Low expression of the NCX makes glioblastoma cells sensitive to disturbance of [Ca²⁺]_i. Interventions designed to block the forward NCX can cause Ca²⁺‐mediated injury to glioblastoma thus having therapeutic potential. Bepridil could be a lead compound for developing new anti‐tumour drugs.

The effect of leflunomide on the transplanted endometriosis lesions in SD rats

OBJECTIVE

To investigate the effects of the leflunomide (LEF) on the size of the transplanted endometriosis (EMS) lesions and trans- forming growth factor (TGF) -β1gray level in SD rats.

MATERIALS AND METHODS

EMS was surgically induced in rats by autologous trans- plantation and the focal volume was also measured. The rats were divided into three groups: group A: normal SD rats, group B: rats irrigated by one ml-kg⁻¹d⁻¹ saline for three weeks, and group C: rats irrigated by 35 mg-kg⁻¹d⁻¹ LEF for three weeks. The rats were then sacrificed and measured their focal volume and TGF-β1 gray value with immunohistochemical method.

RESULTS

The sizes of the focal volume in group C were significantly reduced compared to the rats before feeding, and the volume in group C was smaller than group B after feeding and so was the TGF-β1.

CONCLUSION

LEF could be a new therapeutic drug for EMS.

High-precision evaluation of Wigner's d matrix by exact diagonalization

The precise calculations of Wigner's d matrix are important in various research fields. Due to the presence of large numbers, direct calculations of the matrix using Wigner's formula suffer from a loss of precision. We present a simple method to avoid this problem by expanding the d matrix into a complex Fourier series and calculate the Fourier coefficients by exactly diagonalizing the angular momentum operator J(y) in the eigenbasis of J(z). This method allows us to compute the d matrix and its various derivatives for spins up to a few thousand. The precision of the d matrix from our method is about 10(-14) for spins up to 100.

Activation of muscarinic receptors protects against retinal neurons damage and optic nerve degeneration in vitro and in vivo models

AIMS

Muscarinic acetylcholine receptor agonist pilocarpine reduces intraocular pressure (IOP) of glaucoma mainly by stimulating ciliary muscle contraction and then increasing aqueous outflow. It is of our great interest to know whether pilocarpine has the additional properties of retinal neuroprotection independent of IOP lowering in vitro and in vivo models.

METHODS

In rat primary retinal cultures, cell viability was measured using an MTT assay and the trypan blue exclusion method, respectively. Retinal ganglion cells (RGCs) were identified by immunofluorescence and quantified by flow cytometry. For the in vivo study, the retinal damage after retinal ischemia/reperfusion injury in rats was evaluated by histopathological study using hematoxylin and eosin staining, transmission electron microscopy, and immunohistochemical study on cleaved caspase-3, caspase-3, and ChAT.

RESULTS

Pretreatment of pilocarpine attenuated glutamate-induced neurotoxicity of primary retinal neurons in a dose-dependent manner. Protection of pilocarpine in both retinal neurons and RGCs was largely abolished by the nonselective muscarinic receptor antagonist atropine and the M1-selective muscarinic receptor antagonist pirenzepine. After ischemia/reperfusion injury in retina, the inner retinal degeneration occurred including ganglion cell layer thinning and neuron lost, and the optic nerve underwent vacuolar changes. These degenerative changes were significantly lessened by topical application of 2% pilocarpine. In addition, the protective effect of pilocarpine on the ischemic rat retina was favorably reflected by downregulating the expression of activated apoptosis marker cleaved caspase-3 and caspase-3 and upregulating the expression of cholinergic cell marker ChAT.

CONCLUSIONS

Taken together, this highlights pilocarpine through the activation of muscarinic receptors appear to afford significant protection against retinal neurons damage and optic nerve degeneration at clinically relevant concentrations. These data also further support muscarinic receptors as potential therapeutic neuroprotective targets in glaucoma.

Expression of neuroglobin in ocular hypertension induced acute hypoxic-ischemic retinal injury in rats

AIM

To investigate the expression of neuroglobin (Ngb) in the retina of rats with ocular hypertension induced acute retinal hypoxic-ischemic injury.

METHODS

Seventy Wistar rats were divided into 7 groups randomly. The experimental model was induced by elevation of intraocular pressure via anterior chamber canula insertion in the left eyes and the fellow eyes were preserved as normal controls. The retinal tissues were taken at 1, 5, 10, 15, 20, 30 and 60 minutes after hypoxic-ischemia injury. Protein was extracted, and then analyzed by Western-blot method. SPSS was used for statistical analysis.

RESULTS

The time-depended expressions of Ngb were observed. The level of Ngb increased rapidly at 1 minute after ischemia and reached to the peak at 5 minutes, which had significant difference from that of control group (P<0.05). It kept in high level during 5-15 minutes (P<0.05), then decreased after 20 minutes till 60 minutes. There were no significant differences between experimental and control group in the latter period (P>0.05).

CONCLUSION

The expression of Ngb in retinal tissue increased rapidly after hypoxic-ischemic injury in rats, suggesting that Ngb may play an important role in the process of acute retinal hypoxic-ischemic injury.

Quantitative determination of a novel enantiomeric tropane analog, (-)-satropane, in biological fluids using liquid chromatography/tandem mass spectrometry

A sensitive, accurate and precise liquid chromatography-tandem mass spectrometry method was developed for the determination of (-)-satropane (3alpha-paramethyl-benzenesulfonyloxy-6beta-acetoxy-tropane) in rabbit aqueous humor. Since (-)-satropane may be absorbed from the aqueous humour with resultant systemic side effects, the LC-MS/MS method was also evaluated for its applicability in analyzing plasma samples containing this compound. (-)-Satropane and phentolamine (the internal standard, represented as IS) were detected by multiple reaction monitoring using the transitions m/z 354-182 and 282-212, respectively. The calibration curve was linear over the ranges 2-500 and 5-1000 ng/mL, and the values of the lower limit of quantification were 2 and 5 ng/mL for the microdialysis dialysate and rat plasma samples, respectively. The intra-day and inter-day precision and accuracy were better than 8.6 and 6.00%, respectively, in both matrices investigated. The absolute recovery of the plasma samples was more than 76.30%. The average matrix effects of (-)-satropane were 91.72 and 83.05% in the microdialysis dialysate and plasma samples, respectively. The validated method was successfully applied to analyze (-)-satropane in microdialysis dialysate and rat plasma samples, and this assay has been used to quantify (-)-satropane in the pharmacokinetic and toxicokinetic studies in our laboratory.

Image analysis for monitoring the barley tempeh fermentation process

AIMS

To develop a fast, accurate, objective and nondestructive method for monitoring barley tempeh fermentation.

METHODS AND RESULTS

Barley tempeh is a food made from pearled barley grains fermented with Rhizopus oligosporus. Rhizopus oligosporus growth is important for tempeh quality, but quantifying its growth is difficult and laborious. A system was developed for analysing digital images of fermentation stages using two image processing methods. The first employed statistical measures sensitive to image colour and surface structure, and these statistical measures were highly correlated (r=0.92, n=75, P<0.001) with ergosterol content of tempeh fermented with R. oligosporus and lactic acid bacteria (LAB). In the second method, an image-processing algorithm optimized to changes in images of final tempeh products was developed to measure number of visible barley grains. A threshold of 5 visible grains per Petri dish indicated complete tempeh fermentation. When images of tempeh cakes fermented with different inoculation levels of R. oligosporus were analysed the results from the two image processing methods were in good agreement.

CONCLUSION

Image processing proved suitable for monitoring barley tempeh fermentation. The method avoids sampling, is nonintrusive, and only requires a digital camera with good resolution and image analysis software.

SIGNIFICANCE AND IMPACT OF THE STUDY

The system provides a rapid visualization of tempeh product maturation and qualities during fermentation. Automated online monitoring of tempeh fermentation by coupling automated image acquisition with image processing software could be further developed for process control.

Cytotoxicity and alteredc-myc gene expression by medical polyacrylamide hydrogel

Medical Polyacrylamide Hydrogel (PAMG)has been used in plastic and aesthetic surgery for years. However, its safety is still in doubt in many countries. In the current research, first an approach, using high performance liquid chromatography (HPLC), to determine the amount of residual acrylamide monomer (AM) in the PAMG was presented. Then the cytotoxicity of PAMG was investigated using cell counting and methyl thiazolyl tetrazolium (MTT) assay. To explore the mechanism of this toxicity, normal human fibroblasts cultured in medium extracts were analyzed. Membrane changes and other related parameters were investigated using flow cytometry (FCM). Real time fluorescent polymerase chain reaction (real time PCR) was also introduced to determine the biological response of the fibroblasts. During this process, three representative genes (p53, beta-actin, and c-myc, which are tumor suppressor genes, housekeeping genes, and proto-oncogenes respectively) were selected for examination. Results indicated that a method based on HPLC is practical and simple for determining AM in PAMG. The detection limits can reach the desired ppb level, and so it can fully meet the requirements of the studies of PAMG. Polyacylamide Hydrogel inhibits the growth of human fibroblasts and may cause the apoptosis of human fibroblasts. Moreover, it can alter physical parameters such as the size and the granularity of these cells. Furthermore, these three genes have a relatively typical amplification plot and highly related, wide-range standard curves, and so this reaction system is definitely suitable for the semiquantification of these genes. PAMG induces the increase of the message ribonucleic acid (mRNA) expression of c-myc, while the p53 and beta-actin remain even. This change is not related to the concentration of AM in the gel and may be incited by other components in the extract of PMAG.

Supracondylar extension fracture of the humerus in children. Manipulative reduction, immobilisation and fixation using a U-shaped plaster slab with the elbow in full extension

We present a method of manipulative reduction, immobilisation and fixation using a U-shaped plaster with the elbow in extension for extension-type supracondylar fractures of the humerus in children. When the elbow is in full extension, both the extensor and the flexor muscles are neutralised during manipulative reduction and the carrying angle can be easily assessed thus preventing cubitus varus, the most common complication. In order to evaluate the efficiency of this method, we compared the clinical results of the new method with those of conventional treatment. In a group of 95 children who sustained an extension-type supracondylar fracture of the humerus, 49 were treated by the new method and 46 by the conventional method, reduction and immobilisation in a plaster slab with the elbow in flexion. Reduction and immobilisation were easily achieved and reliably maintained by one manipulation for all the children treated by the new method. In 12 children treated by the conventional method, the initial reduction failed and in seven secondary displacement of the distal fragment occurred during the period of immobilisation in plaster. All required a second or third manipulation. Of the 46 children, 28 (60.9%) had developed cubitus varus at a mean follow-up of 4.6 years when treated by the conventional method. None of the children treated by the new method developed cubitus varus. The mean score, according to the Hospital for Special Surgery (HSS) elbow scoring system, was 91 points using the new method and 78 with the conventional method. The results were statistically significant with regard to the incidence of cubitus varus and the elbow score (p < 0.01) suggesting that the new method is reliable and gives a satisfactory outcome.

A novel AvaI polymorphism within exon 5 of the rhodopsin gene

We identified a novel AvaI polymorphism within 3' non-coding region within exon 5 of the human rhodopsin gene and determined the allele frequency in a Japanese population. The polymorphism was found to be due to A/G transversion at nucleotide 5510 of the gene.

Inhibition of hepatitis B virus in vitro by antisense oligonucleotides

A series of antisense phosphorothioate oligodeoxynucleotides against hepatitis B virus (HBV) were synthesized and evaluated for their antiviral effect in Hep-G2 cells transfected with HBV genome. The inhibitory effect of the tested antisense oligonucleotides was sequence-specific, dose-and time-dependent, and synergistic for certain combinations. In virus-inhibitory concentrations the oligonucleotides were harmless to 2.2.15 cells. The most effective antisense oligonucleotides were found directed against the HBV mRNA transcribed from the cap site of SP II promoter, the portion of polyadenylation signal and the initiation region of gene S, with an inhibition of the HBsAg and HBeAg production by 85-95% and 50- 60%, respectively. To our surprise, antisense oligonucleotides directed against three key sites of HBV X gene blocked the expression of HBsAg, HBeAg and HBxAg. This fact might be related to the trans-activation of HBV X protein. Using radioisotope labelling, we demonstrated that Lipofectin promoted the cellular uptake and antiviral effect of antisense oligomers in 2.2.15 cells. These results suggest a therapeutic potential of antisense oligonucleotides in the treatment of patients chronically infected with HBV.

Specific inhibition of hepatitis b virus gene expression by an antisense oligonucleotide in vitro

It was previously shown that a number of antisense oligonucleotides against hepatitis B virus (HBV) mRNAs were highly effective in inhibition of HBV gene expression (Yao et al., 1995). Here, using radioisotope techniques, we report a specific inhibition of HBV surface antigen (HBsAg) production in vitro by 2.2.15 cells (Hep-G2 cells transfected with HBV genome) by the antisense oligonucleotide 15-S-asON, a 15-mer phosphorothioate analogue complementary to the cap site of the SPII promoter of HBV mRNA, at a concentration of 2-5 mumol/l. After 24 and 48 hrs of incubation of cells with 15-S-asON, the intracellular concentration of the latter rose to 69.4 and 75.8 nmol/l, respectively, and the HBsAg level assayed by ELISA was reduced by 50.0% and 70.6%, respectively. These results were checked by use of the radioimmunoprecipitation method: 2.2.15 cells exposed to 15-S-asON and labelled with [35S]-methionine for 48 hrs showed a decrease of the HBsAg level by 81.26% but almost none of the total proteins. No cytotoxicity of the 15-S-asON was observed with regard to the cell morphology and growth. These results indicate that the tested antisense oligonucleotide specifically inhibits the HBV gene expression.