APA-Scan: detection and visualization of 3'-UTR alternative polyadenylation with RNA-seq and 3'-end-seq data

Background

The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3′-untranslated region (3′-UTR) of mRNA produces transcripts with shorter or longer 3′-UTR. Often, 3′-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3′-UTR APA is known to modulate translation and provides a mean to regulate gene expression at the post-transcriptional level. Current bioinformatics pipelines have limited capability in profiling 3′-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3′-UTR APA only using RNA-seq read coverage, causing false positive identifications. To overcome these limitations, we developed APA-Scan, a robust program that identifies 3′-UTR APA events and visualizes the RNA-seq short-read coverage with gene annotations.

Methods

APA-Scan utilizes either predicted or experimentally validated actionable polyadenylation signals as a reference for polyadenylation sites and calculates the quantity of long and short 3′-UTR transcripts in the RNA-seq data. APA-Scan works in three major steps: (i) calculate the read coverage of the 3′-UTR regions of genes; (ii) identify the potential APA sites and evaluate the significance of the events among two biological conditions; (iii) graphical representation of user specific event with 3′-UTR annotation and read coverage on the 3′-UTR regions. APA-Scan is implemented in Python3. Source code and a comprehensive user’s manual are freely available at https://github.com/compbiolabucf/APA-Scan.

Result

APA-Scan was applied to both simulated and real RNA-seq datasets and compared with two widely used baselines DaPars and APAtrap. In simulation APA-Scan significantly improved the accuracy of 3′-UTR APA identification compared to the other baselines. The performance of APA-Scan was also validated by 3′-end-seq data and qPCR on mouse embryonic fibroblast cells. The experiments confirm that APA-Scan can detect unannotated 3′-UTR APA events and improve genome annotation.

Conclusion

APA-Scan is a comprehensive computational pipeline to detect transcriptome-wide 3′-UTR APA events. The pipeline integrates both RNA-seq and 3′-end-seq data information and can efficiently identify the significant events with a high-resolution short reads coverage plots.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04939-w.

Platform-integrated mRNA isoform quantification

MOTIVATION

Accurate estimation of transcript isoform abundance is critical for downstream transcriptome analyses and can lead to precise molecular mechanisms for understanding complex human diseases, like cancer. Simplex mRNA Sequencing (RNA-Seq) based isoform quantification approaches are facing the challenges of inherent sampling bias and unidentifiable read origins. A large-scale experiment shows that the consistency between RNA-Seq and other mRNA quantification platforms is relatively low at the isoform level compared to the gene level. In this project, we developed a platform-integrated model for transcript quantification (IntMTQ) to improve the performance of RNA-Seq on isoform expression estimation. IntMTQ, which benefits from the mRNA expressions reported by the other platforms, provides more precise RNA-Seq-based isoform quantification and leads to more accurate molecular signatures for disease phenotype prediction.

RESULTS

In the experiments to assess the quality of isoform expression estimated by IntMTQ, we designed three tasks for clustering and classification of 46 cancer cell lines with four different mRNA quantification platforms, including newly developed NanoString's nCounter technology. The results demonstrate that the isoform expressions learned by IntMTQ consistently provide more and better molecular features for downstream analyses compared with five baseline algorithms which consider RNA-Seq data only. An independent RT-qPCR experiment on seven genes in twelve cancer cell lines showed that the IntMTQ improved overall transcript quantification. The platform-integrated algorithms could be applied to large-scale cancer studies, such as The Cancer Genome Atlas (TCGA), with both RNA-Seq and array-based platforms available.

AVAILABILITY AND IMPLEMENTATION

Source code is available at: https://github.com/CompbioLabUcf/IntMTQ.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A large-scale comparative study of isoform expressions measured on four platforms

BACKGROUND

Most eukaryotic genes produce different transcripts of multiple isoforms by inclusion or exclusion of particular exons. The isoforms of a gene often play diverse functional roles, and thus it is necessary to accurately measure isoform expressions as well as gene expressions. While previous studies have demonstrated the strong agreement between mRNA sequencing (RNA-seq) and array-based gene and/or isoform quantification platforms (Microarray gene expression and Exon-array), the more recently developed NanoString platform has not been systematically evaluated and compared, especially in large-scale studies across different cancer domains.

RESULTS

In this paper, we present a large-scale comparative study among RNA-seq, NanoString, array-based, and RT-qPCR platforms using 46 cancer cell lines across different cancer types. The goal is to understand and evaluate the calibers of the platforms for measuring gene and isoform expressions in cancer studies. We first performed NanoString experiments on 59 cancer cell lines with 404 custom-designed probes for measuring the expressions of 478 isoforms in 155 genes, and additional RT-qPCR experiments for a subset of the measured isoforms in 13 cell lines. We then combined the data with the matched RNA-seq, Exon-array, and Microarray data of 46 of the 59 cell lines for the comparative analysis.

CONCLUSION

In the comparisons of the platforms for measuring the expressions at both isoform and gene levels, we found that (1) the agreement on isoform expressions is lower than the agreement on gene expressions across the four platforms; (2) NanoString and Exon-array are not consistent on isoform quantification even though both techniques are based on hybridization reactions; (3) RT-qPCR experiments are more consistent with RNA-seq and Exon-array than NanoString in isoform quantification; (4) different RNA-seq isoform quantification methods show varying estimation results, and among the methods, Net-RSTQ and eXpress are more consistent across the platforms; and (5) RNA-seq has the best overall consistency with the other platforms on gene expression quantification.

mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control

U2 auxiliary factor 1 (U2AF1) functions in 3′-splice site selection during pre-mRNA processing. Alternative usage of duplicated tandem exons in U2AF1 produces two isoforms, U2AF1a and U2AF1b, but their functional differences are unappreciated due to their homology. Through integrative approaches of genome editing, customized-transcriptome profiling and crosslinking-mediated interactome analyses, we discovered that the expression of U2AF1 isoforms is controlled by mTOR and they exhibit a distinctive molecular profile for the splice site and protein interactomes. Mechanistic dissection of mutually exclusive alternative splicing events revealed that U2AF1 isoforms’ inherent differential preferences of nucleotide sequences and their stoichiometry determine the 3′-splice site. Importantly, U2AF1a-driven transcriptomes feature alternative splicing events in the 5′-untranslated region (5′-UTR) that are favorable for translation. These findings unveil distinct roles of duplicated tandem exon-derived U2AF1 isoforms in the regulation of the transcriptome and suggest U2AF1a-driven 5′-UTR alternative splicing as a molecular mechanism of mTOR-regulated translational control.

A Comparative Study of E-Beam Deposited Gate Dielectrics on Channel Width-Dependent Performance and Reliability of a-IGZO Thin-Film Transistors

A comparative study on the effects of e-beam deposited gate dielectrics for amorphous indium gallium zinc oxide (a-IGZO) thin-film transistors (TFTs) has been carried out using SiO₂, Si₃N₄, and Ta₂O₅ dielectric materials. The channel width dependent device electrical performances were investigated using three different sizes of 500 μm, 1000 μm, and 1500 μm. The reliability characteristics were revealed by the threshold voltage variation and drain current variation under positive bias stress. The e-beam deposited high-k dielectric Ta₂O₅ exhibited the highest stability at the stress voltage of 3 V for 1000 s due to its high capacitance density at 34.1 nF/cm². The threshold voltage variation along the channel width decreased from SiO₂, then Si₃N₄, to Ta₂O₅, because of the increased insulating property and density of capacitance. The SiO₂-based a-IGZO TFT achieved a high field effect mobility of 27.9 cm²/V·s and on⁻off current ratio > 10⁷ at the lower channel width of 500 μm. The gate leakage current also decreased with increasing the channel width/length ratio. In addition, the SiO₂ gate dielectric-based a-IGZO TFT could be a faster device, whereas the Ta₂O₅ gate dielectric would be a good candidate for a higher reliability component with adequate surface treatment.

Systematic review and meta-regressions: management of eosinophilic esophagitis requires histologic assessment

Treatment endpoints in eosinophilic esophagitis (EoE) are response of eosinophilic inflammation and of symptoms. Steroids and diet therapy are effective in inducing histologic response in EoE, but there may be poor correlation between histologic and symptomatic response. Despite this, we find that in clinical practice symptoms are commonly used to guide management without assessing histologic response. We hypothesized that symptom response alone is not reliable in assessing response to therapy and is confounded by endoscopic dilation. We conducted a systematic review and meta-regressions to estimate the association of histologic and symptomatic response, stratified by whether concurrent dilation was permitted. We performed a systematic search of PubMed, EMBASE, and Web of Science for studies describing both histologic and symptomatic responses to dilation, steroid, and diet therapies. We abstracted the proportion of histologic response and symptom response. Studies were stratified by whether dilation was permitted. We performed meta-regressions of the association between the proportions with histologic and symptomatic response, stratified by whether dilation was permitted. We identified 1359 articles, of which 62 articles were assessed for eligibility, and 23 were included providing data on 1202 patients with EoE. Unstratified meta-regression of histologic versus symptomatic response showed moderate association and large heterogeneity (inconsistency index [I2] = 89%). In adult studies in which dilation was allowed, there was weak association between symptomatic and histologic response (β1 = 0.21), minimal symptomatic response of 67% and the heterogeneity persisted, I2 = 77%. In studies that prohibited dilation, maximal symptomatic response was 72% and was moderately associated with histologic response (β1 = 0.39) with less heterogeneity, I2 = 59%. Studies of EoE that permit dilation obscure the relation between histologic and symptomatic response and have a high floor effect for symptomatic response. Studies that prohibit dilation demonstrate moderate association between histologic and symptomatic response, but have a ceiling effect for symptomatic response. Our results demonstrate that success of dietary or medical management for EoE cannot be judged by symptoms alone, and require histologic assessment, particularly if dilation has been performed.

An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response

3'-untranslated regions (UTRs) can vary through the use of alternative polyadenylation sites during pre-mRNA processing. Multiple publically available pipelines combining high profiling technologies and bioinformatics tools have been developed to catalog changes in 3'-UTR lengths. In our recent RNA-seq experiments using cells with hyper-activated mammalian target of rapamycin (mTOR), we found that cellular mTOR activation leads to transcriptome-wide alternative polyadenylation (APA), resulting in the activation of multiple cellular pathways. Here, we developed a novel bioinformatics algorithm, IntMAP, which integrates RNA-Seq and PolyA Site (PAS)-Seq data for a comprehensive characterization of APA events. By applying IntMAP to the datasets from cells with hyper-activated mTOR, we identified novel APA events that could otherwise not be identified by either profiling method alone. Several transcription factors including Cebpg (CCAAT/enhancer binding protein gamma) were among the newly discovered APA transcripts, indicating that diverse transcriptional networks may be regulated by mTOR-coordinated APA. The prevention of APA in Cebpg using the CRISPR/cas9-mediated genome editing tool showed that mTOR-driven 3'-UTR shortening in Cebpg is critical in protecting cells from endoplasmic reticulum (ER) stress. Taken together, we present IntMAP as a new bioinformatics algorithm for APA analysis by which we expand our understanding of the physiological role of mTOR-coordinated APA events to ER stress response. IntMAP toolbox is available at http://compbio.cs.umn.edu/IntMAP/.

Injecting NMDA and Ro 25-6981 in insular cortex induce neuroplastic changes and neuropathic pain-like behaviour

BACKGROUND

Neuropathic pain is associated with abnormal sensitivity of the central nervous system. Although the mechanism underlying the development of sensitization remains to be fully elucidated, recent studies have reported that neuroplastic changes in the pain circuitry may be involved in hypersensitivity associated with neuropathic pain. However, it is difficult to investigate such phenomena in existing animal pain model. Therefore, in this study, we developed a novel animal model - the circuit plasticity reconstruction (CPR) model - to mimic central sensitization associated with neuroplastic changes.

METHOD

NMDA and Ro 25-6981 were injected into the right insular cortex of Sprague-Dawley rats, while electrical stimulation was delivered to the contralateral hind paw. Mechanical allodynia was tested by von Frey test with up-down method, and neuroplastic changes were confirmed by PSA-NCAM-positive immunostaining.

RESULT

The mechanical withdrawal threshold of the left hind paw decreased beginning 1 day after CPR modelling and persisted until day 21 comparing to the modified CPR 1 (mod-CPR 1) group (CPR: 91.68 ± 1.8%, mod-CPR 1: 42.71 ± 3.4%, p < 0.001). In contrast, mod-CPR 2 surgery without electrical stimulation did not induce mechanical allodynia. Immunostaining for PSA-NCAM also revealed that neuroplastic changes had occurred in the CPR group.

CONCLUSION

Our results demonstrated that CPR modelling induced neuroplasticity within the insular cortex, leading to alterations in the neural circuitry and central sensitization.

SIGNIFICANCE

This article represents that the CPR model can mimic the neuropathic pain derived by neuroplastic changes. Our findings indicate that the CPR model may aid the development of novel therapeutic strategies for neuropathic pain and in elucidating the mechanisms underlying pain induced by central sensitization and neuroplastic changes.

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-Seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification. Net-RSTQ toolbox is available at http://compbio.cs.umn.edu/Net-RSTQ/.

Bilateral thermal capsulotomy with MR-guided focused ultrasound for patients with treatment-refractory obsessive-compulsive disorder: a proof-of-concept study

Despite optimal pharmacotherapy and cognitive-behavioral treatments, a proportion of patients with obsessive-compulsive disorder (OCD) remain refractory to treatment. Neurosurgical ablative or nondestructive stimulation procedures to treat these refractory patients have been investigated. However, despite the potential benefits of these surgical procedures, patients show significant surgery-related complications. This preliminary study investigated the use of bilateral thermal capsulotomy for patients with treatment-refractory OCD using magnetic resonance-guided focused ultrasound (MRgFUS) as a novel, minimally invasive, non-cranium-opening surgical technique. Between February and May 2013, four patients with medically refractory OCD were treated with MRgFUS to ablate the anterior limb of the internal capsule. Patients underwent comprehensive neuropsychological evaluations and imaging at baseline, 1 week, 1 month and 6 months following treatment. Outcomes were measured with the Yale-Brown Obsessive-Compulsive Scale (Y-BOCS), the Hamilton Rating Scale for Depression (HAM-D) and the Hamilton Rating Scale for Anxiety (HAM-A), and treatment-related adverse events were evaluated. The results showed gradual improvements in Y-BOCS scores (a mean improvement of 33%) over the 6-month follow-up period, and all patients showed almost immediate and sustained improvements in depression (a mean reduction of 61.1%) and anxiety (a mean reduction of 69.4%). No patients demonstrated any side effects (physical or neuropsychological) in relation to the procedure. In addition, there were no significant differences found in the comprehensive neuropsychological test scores between the baseline and 6-month time points. This study demonstrates that bilateral thermal capsulotomy with MRgFUS can be used without inducing side effects to treat patients with medically refractory OCD. If larger trials validate the safety, effectiveness and long-term durability of this new approach, this procedure could considerably change the clinical management of treatment-refractory OCD.

Identification of glucose-6-phosphate transporter as a key regulator functioning at the autophagy initiation step

Autophagy is a catabolic process involving autophagosome formation via lysosome. However, the initiation step of autophagy is largely unknown. We found an interaction between ULK1 and ATG9 in mammalian cells and utilized the interaction to identify novel regulators of autophagy upstream of ULK1. We established a cell-based screening assay employing bimolecular fluorescence complementation. By performing gain-of-function screening, we identified G6PT as an autophagy activator. G6PT enhanced the interaction between N-terminal Venus-tagged ULK1 and C-terminal Venus-tagged ATG9, and increased autophagic flux independent of its transport activity. G6PT negatively regulated mTORC1 activity, demonstrating that G6PT functions upstream of mTORC1 in stimulating autophagy.

BECN1/Beclin 1 is recruited into lipid rafts by prion to activate autophagy in response to amyloid β 42

Prion protein (PRNP) has been implicated in various types of neurodegenerative diseases. Although much is known about prion diseases, the function of cellular PRNP remains cryptic. Here, we show that PRNP mediates amyloid β1–42 (Aβ42)-induced autophagy activation through its interaction with BECN1. Treatment with Aβ42 enhanced autophagy flux in neuronal cells. Aβ42-induced autophagy activation, however, was impaired in prnp-knockout primary cortical neurons and Prnp-knockdown or prnp-knockout neuronal cells. Immunoprecipitation assays revealed that PRNP interacted with BECN1 via the BCL2-binding domain of BECN1. This interaction promoted the subcellular localization of BECN1 into lipid rafts of the plasma membrane and enhanced activity of PtdIns3K (whose catalytic subunit is termed PIK3C3, mammalian ortholog of yeast VPS34) in lipid rafts by generating PtdIns3P in response to Aβ42. Further, the levels of lipid rafts that colocalized with BECN1, decreased in the brains of aged C57BL/6 mice, as did PRNP. These results suggested that PRNP interacts with BECN1 to recruit the PIK3C3 complex into lipid rafts and thus activates autophagy in response to Aβ42, defining a novel role of PRNP in the regulation of autophagy.

Characterization and analysis of finite-beam Bragg diffraction in a periodically poled lithium niobate electro-optic grating

We report the study, both theoretical and experimental, of the finite-beam Bragg diffraction behavior of an electro-optic (EO) volume grating made of a periodically poled lithium niobate (PPLN) crystal. When a Gaussian laser beam is used, the experimental observations show that the diffraction characteristics of the PPLN EO Bragg device, including the diffraction mode pattern and diffraction efficiency, are closely related to the interaction beam size and applied voltage, which cannot be modeled properly by a simplified theory using the plane-wave approximation. In this work, we have developed a theoretical model for describing the diffraction behavior of a PPLN EO Bragg device based on the coupled-wave theory with the aid of the plane-wave decomposition method. Specifically, we found that it is the angular distribution (or the dephasing bandwidth) of the plane wave elements decomposed from the incident Gaussian beam and grating strength that determine the Bragg coupling behavior of the device. We also identified some other electro-optically induced effects in the PPLN grating as an important mechanism in affecting the diffraction performance of the present device, especially at high working voltages.

Cumulative risk assessment for plasticizer-contaminated food using the hazard index approach

Phthalates strongly and adversely affect reproduction, development and liver function. We did a cumulative risk assessment for simultaneous exposure to nine phthalates using the hazard index (HI) and the levels of nine phthalates in 1200 foodstuff samples. DEHP (di-2-ethylhexyl phthalate) present the highest level (mean: 0.443 mg/kg) in 1200 samples, and the highest average daily dose (ADD) was found in DEHP, ΣDBP(i + n) (the sum of dibutyl phthalate [DBP] isomers [DnBP + DiBP]) posed the highest risk potential of all the phthalates. In seven phthalates, the 95th percentiles of the ADDs for ΣDBP(i + n) in 0-6-yr-old children accounted for 91% (79-107%) of the tolerable daily intake, and the 95th percentiles of the HIs for the anti-androgenic effects of five phthalates in 0-3-yr-old children and 4-6-yr-old girls were >1. We conclude that the health of younger Taiwanese may be adversely affected by overexposure of phthalate-contaminated foods.

Double-prism domain PPLN for simultaneous laser Q-switching and optical parametric oscillation in a Nd:YVO4 laser

We report a design and demonstration of an electro-optically Q-switched intracavity optical parametric oscillator (IOPO) based on a unique ramped duty-cycle periodically poled lithium niobate (PPLN) in a diode-pumped 1064-nm Nd:YVO(4) laser. The PPLN crystal, having a double-prism domain (DPD) structure with a domain period of 30 μm, can work simultaneously as an electro-optic (EO) beam deflector (and therefore an EO Q-switch in the laser cavity) and an optical parametric down converter. The characterized deflection sensitivity of the DPD PPLN device was 1.15°/kV-cm. At a 180-V Q-switching voltage and a 1-kHz switching rate, we measured a down-converted signal at 1550 nm with pulse energy of >8.1 μJ (or peak power of >2.3 kW) from the constructed IOPO at 7.5-W diode pump power. Continuous wavelength tuning of the IOPO signal was also demonstrated.

Tunable, pulsed multiline intracavity optical parametric oscillator using two-dimensional MgO: periodically poled lithium niobate-aperiodically poled lithium niobate

We report a tunable, pulsed multiline intracavity optical parametric oscillator (IOPO) realized in an Nd:YVO4 laser using a two-dimensionally domain engineered MgO:LiNbO3 as simultaneously an electro-optic Bragg Q switch and a multichannel optical parametric downconverter. The MgO:LiNbO3 was periodically and aperiodically poled along the crystallographic y and x axes, respectively, to simultaneously satisfy the phase-matching conditions required by the two quasi-phase-matching devices. When Q switched by 1 kHz, 300 V pulses, three signal lines at 1518, 1526, and 1534 nm were simultaneously generated, each with a peak power of ∼1  kW from the IOPO at 8.3 W diode power at 50°C. Spectral tuning of the three-line IOPO with temperature was demonstrated.

Serum apolipoprotein C-II is prognostic for survival after pancreatic resection for adenocarcinoma

BACKGROUND

Pancreaticoduodenectomy remains a major undertaking. A preoperative blood test, which could confidently predict the benefits of surgery would improve the selection of pancreatic cancer patients for surgery. This study aimed to identify protein biomarkers prognostic for long-term survival and to validate them with clinico-pathological information.

METHODS

Serum from 40 preoperative patients was used to train for predictive biomarkers using surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI), and the results were verified on 21 independent samples. Two predictive proteins were identified by tryptic peptide mass fingerprinting and sequencing, and validated on serum from another 57 patients by enzyme-linked immunosorbent assay (ELISA). The influence of these proteins on growth and invasion of two cancer cell lines was tested in-vitro.

RESULTS

The SELDI panel of m/z 3700, 8222 and 11 522 peaks predicted <12 months' survival (ROC AUC: 0.79, 0.64-0.90; P<0.039). When CA19-9 was added, the ROC AUC increased to 0.95 (0.84-0.99; P<0.0001). The six subjects in the verification group who died within 12 months were correctly classified. The m/z 8222 and 11 522 proteins were identified as Serum ApoC-II and SAA-1, respectively. In the validation samples, ELISA results confirmed that ApoC-II was predictive of survival (Kaplan-Meier P<0.009), but not SAA-I. ApoC-II, CA19-9 and major-vessel involvement independently predicted survival. ApoC-II and SAA-1 increased cell growth and invasion of both cancer cell lines.

CONCLUSION

Serum ApoC-II, CA19-9 and major-vessel invasion independently predict survival and improves selection of patients for pancreaticoduodenectomy.

Calsenilin contributes to neuronal cell death in ischemic stroke

Calsenilin is a calcium sensor protein that interacts with presenilin and increases calcium-triggered neuronal apoptosis, and γ-secretase activity. Notch is a cell surface receptor that regulates cell-fate decisions and synaptic plasticity in brain. The aim of the present study was to characterize the role of calsenilin as a regulator of the γ-secretase cleavage of Notch in ischemic stroke. Here, we determined the modulation of expression level and cellular distribution of calsenilin in neurons subjected to ischemic-like conditions. The levels of calsenilin and presenilin were increased in primary neurons after oxygen and glucose deprivation. Furthermore, calsenilin was found to enhance the γ-secretase cleavage of Notch and to contribute to cell death under ischemia-like conditions. The inhibition of γ-secretase activity and a presenilin deficiency were both found to protect against calsenilin-mediated ischemic neuronal death. The expression of calsenilin was found to be increased in brain following experimental ischemic stroke. These findings establish a specific molecular mechanism by which the induction of calsenilin enhances Notch activation in ischemic stroke, and identify calsenilin as an upstream of the γ-secretase cleavage of Notch.

Electro-optically tunable, multi-wavelength optical parametric generators in aperiodically poled lithium niobates

We report on the design and demonstration of electro-optically tunable, multi-wavelength optical parametric generators (OPGs) based on aperiodically poled lithium niobate (APPLN) crystals. Two methods have been proposed to significantly enhance the electro-optic (EO) tunability of an APPLN OPG constructed by the aperiodic optical superlattice (AOS) technique. This is done by engineering the APPLN domain structure either in the crystal fabrication or in the crystal design process to increase the length or block-number difference of the two opposite-polarity domains used in the structure. Several orders of magnitude enhancement on the EO tuning rate of the APPLN OPGs constructed by the proposed techniques for simultaneous multiple signal wavelength generation over a conventional one has been demonstrated in a near infrared band (1500-1600 nm).

Biochemical study of retired pentachlorophenol workers with and without following dietary exposure to PCDD/Fs

PCDD/Fs are found as impurities in commercial pesticide sodium pentachlorophenol (Na-PCP) salt. We compared, using multivariate logistic regression analysis adjusted for confounding factors, serum PCDD/F levels and biochemical examinations of retired Na-PCP workers and other inhabitants living near a closed Na-PCP plant that discharged PCP-contaminated wastewater into a nearby pond in Tainan, Taiwan. In this cross-sectional study from October 2006 through May 2009, 1167 participants were divided into groups according to their occupational (retired Na-PCP plant workers versus other residents) and dietary exposure (eating polluted fish versus not eating polluted fish) to PCDD/Fs, and a general population from a large-scale survey. Serum PCDD/F levels were significantly different between these groups (range: from 22.9±10.0pg WHO(98)-TEQ(DF) g(-1) lipid in the general population to 109.6±94.5pg WHO(98)-TEQ(DF) g(-1) lipid in retired Na-PCP workers eating polluted seafood; P(trend)<0.001). Distinct patterns of PCDD/Fs congener profiles, showing a significantly higher proportion of 1,2,3,7,8-PeCDD, 1,2,3,6,7,8-HxDD, and less 2,3,4,6,7,8-HpCDF, OCDF, were also found among workers and residents with different serum PCDD/F levels versus the general population. After adjusting for confounding factors, glucose (adjusted odds ratio [AOR] 7.22 [95% CI: 4.04-12.90]), triglycerides (AOR 4.31 [95% CI: 2.57-7.22]), blood urea nitrogen (AOR 2.90 [95% CI: 1.58-5.33]), creatine (AOR 5.83 [95% CI: 1.12-30.30]) and total protein (AOR 3.74 [95% CI: 1.91-7.31]) levels in retired workers were significantly higher than in the reference group. Occupational exposure to PCDD/Fs is associated with biochemical abnormalities that may persist for years after serum PCDD/F levels have declined.

Internal Q-switching and self-optical parametric oscillation in a two-dimensional periodically poled Nd:MgO:LiNbO3 laser

We report on an internally Q-switched self-optical parametric oscillator (SOPO) based on a monolithic two-dimensional (2D) periodically poled Nd:MgO:LiNbO(3) (Nd:MgO:PPLN) integrating three device functionalities of a laser gain medium, an electro-optic Bragg Q-switch, and an optical parametric gain medium (OPGM). The quasi-phase-matching conditions required by the Bragg Q-switch and OPGM are both satisfied in the 2D nonlinear photonic crystal (NPC) structure formed in the Nd:MgO:PPLN. A 1525 nm signal with a pulse energy of ∼3.3 μJ (>350 W peak power) was obtained from the SOPO at 8.5 W diode pump power. An off-angle signal at 1612 nm, amplified by a unique gain-enhancement effect in this 2D NPC, was also observed. Tuning of the SOPO in the eye-safe region was demonstrated.

Two-dimensional PPLN for simultaneous laser Q-switching and optical parametric oscillation in a Nd:YVO4 laser

We report on a tunable intracavity optical parametric oscillator (IOPO) achieved using a two-dimensional (2D) periodically poled lithium niobate (PPLN) as simultaneously an electro-optic (EO) Bragg Q-switch and an optical frequency mixer (OFM) in a diode-pumped Nd:YVO(4) laser. The 2D periodic domain inversion structure is designed to provide two orthogonal reciprocal vectors to respectively satisfy the phase-matching conditions required by the two quasi-phase-matching devices (i.e., the PPLN EO Bragg deflector and the PPLN OFM). At a ~140-V Q-switching voltage and a 1-kHz switching rate, we obtained a signal wave at 1550 nm with a pulse energy of 9.7 μJ (corresponding to a peak power of ~2.4 kW) from the IOPO at 9.1-W diode pump power. Simultaneously we also observed multi-wavelength generation from the system originating in the single-pass parametric conversions in the 2D nonlinear photonic crystal structure. Temperature tuning of the IOPO signal wavelength in the eye-safe region was also demonstrated.

Soluble intracellular adhesion molecule-1 secreted by human umbilical cord blood-derived mesenchymal stem cell reduces amyloid-β plaques

Presently, co-culture of human umbilical cord blood mesenchymal stem cells (hUCB-MSCs) with BV2 microglia under amyloid-β42 (Aβ42) exposure induced a reduction of Aβ42 in the medium as well as an overexpression of the Aβ-degrading enzyme neprilysin (NEP) in microglia. Cytokine array examinations of co-cultured media revealed elevated release of soluble intracellular adhesion molecule-1 (sICAM-1) from hUCB-MSCs. Administration of human recombinant ICAM-1 in BV2 cells and wild-type mice brains induced NEP expression in time- and dose-dependent manners. In co-culturing with BV2 cells under Aβ42 exposure, knockdown of ICAM-1 expression on hUCB-MSCs by small interfering RNA (siRNA) abolished the induction of NEP in BV2 cells as well as reduction of added Aβ42 in the co-cultured media. By contrast, siRNA-mediated inhibition of the sICAM-1 receptor, lymphocyte function-associated antigen-1 (LFA-1), on BV2 cells reduced NEP expression by ICAM-1 exposure. When hUCB-MSCs were transplanted into the hippocampus of a 10-month-old transgenic mouse model of Alzheimer's disease for 10, 20, or 40 days, NEP expression was increased in the mice brains. Moreover, Aβ42 plaques in the hippocampus and other regions were decreased by active migration of hUCB-MSCs toward Aβ deposits. These data suggest that hUCB-MSC-derived sICAM-1 decreases Aβ plaques by inducing NEP expression in microglia through the sICAM-1/LFA-1 signaling pathway.

Recurrent disease following endoscopic ablation of Barrett's high-grade dysplasia with spray cryotherapy

BACKGROUND AND AIMS

Recurrent disease after endoscopic ablation of Barrett's esophagus should be detected early to prevent malignant progression. We assessed the incidence and patterns of disease recurrence in patients after liquid nitrogen spray cryotherapy ablation of Barrett's esophagus with high grade dysplasia (HGD), including the area below the neosquamocolumnar junction (NSCJ).

PATIENTS AND METHODS

This is a single-center, retrospective study of prospectively collected data on consecutive cases of endoscopic ablation with liquid nitrogen spray cryotherapy for Barrett's HGD. Post-treatment surveillance biopsies were obtained of suspicious lesions and in 4 quadrants every 1 cm in the treated esophagus and just below the NSCJ. Primary outcome measures were location and histology of recurrent disease.

RESULTS

36 patients (median age 62 years, 92% men) were enrolled, and 11 (30%) developed recurrent disease in a median of 6.5 months; three developed a second recurrence. Ten recurrences (71%) were identified below the NSCJ in 9 patients, including HGD (4), low grade dysplasia (LGD) (2), and intestinal metaplasia (4). Six recurrences were identified in the treated esophagus in five patients, including intramucosal cancer (1), HGD (1), and intestinal metaplasia (4). Two patients had recurrent disease involving both locations. Ultimately 33 patients (92%) achieved a complete response. Diagnosis in the remaining three was LGD (1) and intestinal metaplasia (2).

CONCLUSION

Most patients with recurrent intestinal metaplasia with or without dysplasia after ablation achieve a complete response. Recurrent disease commonly involves the area just below the NSCJ. Surveillance endoscopies should include this area to accurately identify patients with disease recurrence.

IRE1 plays an essential role in ER stress-mediated aggregation of mutant huntingtin via the inhibition of autophagy flux

Huntington's disease (HD), an inherited neurodegenerative disorder, is caused by an expansion of cytosine-adenine-guanine repeats in the huntingtin gene. The aggregation of mutant huntingtin (mtHTT) and striatal cell loss are representative features to cause uncontrolled movement and cognitive defect in HD. However, underlying mechanism of mtHTT aggregation and cell toxicity remains still elusive. Here, to find new genes modulating mtHTT aggregation, we performed cell-based functional screening using the cDNA expression library and isolated IRE1 gene, one of endoplasmic reticulum (ER) stress sensors. Ectopic expression of IRE1 led to its self-activation and accumulated detergent-resistant mtHTT aggregates. Treatment of neuronal cells with ER stress insults, tunicamycin and thapsigargin, increased mtHTT aggregation via IRE1 activation. The kinase activity of IRE1, but not the endoribonuclease activity, was necessary to stimulate mtHTT aggregation and increased death of neuronal cells, including SH-SY5Y and STHdhQ111/111 huntingtin knock-in striatal cells. Interestingly, ER stress impaired autophagy flux via IRE1-TRAF2 pathway, thus enhancing cellular accumulation of mtHTT. Atg5 deficiency in M5-7 cells increased mtHTT aggregation but blocked ER stress-induced mtHTT aggregation. Further, ER stress markers including p-IRE1 and autophagy markers such as p62 were up-regulated exclusively in the striatal tissues of HD mouse models and in HD patients. Moreover, down-regulation of IRE1 expression rescues the rough-eye phenotype by mtHTT in a HD fly model. These results suggest that IRE1 plays an essential role in ER stress-mediated aggregation of mtHTT via the inhibition of autophagy flux and thus neuronal toxicity of mtHTT aggregates in HD.

Variations in the course of the cervical vagus nerve on thyroid ultrasonography

BACKGROUND AND PURPOSE

Only 1 ultrasonography study that described the variation of the VN had been published at the time our research was begun. The purpose of this study was to evaluate the incidence and type of variation in the course of the cervical VN on thyroid ultrasonography.

MATERIALS AND METHODS

From August 2009 to September 2010, 163 consecutive patients were evaluated by sonography for the screening and characterization of thyroid nodules (mean age, 49.0 ± 14.4 years, male:female, 20:143). Two types of variation were defined as follows: 1) anterior variation, when the course of the VNs changed from the typical location to an anterior location in front of the CCA; and 2) medial variation, when the course of the VNs changed from the typical location to a location medial to the CCA (between CCA and thyroid gland). The incidence of the each variation was studied.

RESULTS

Variation in the course of the VN occurred in 5.5% (18/326) of cases. The anterior variation was observed in 4.3% (14/326, right:left = 4:10), and the medial variation was observed in 1.2% (4/326, right:left = 3:1). For both variations, the VN was close to or nearly abutted the thyroid gland after it changed course.

CONCLUSIONS

Variation in the course of the cervical VN could be assessed by ultrasonography. Two variations were observed in 5.5% of cases. The anterior variation was more common than the medial variation.

EZH2 silencing by RNA interference inhibits proliferation in bladder cancer cell lines

The Enhancer of Zeste homologue2 gene (EZH2) is frequently expressed at high levels in malignant tumours, including bladder cancer. It functions as a transcriptional regulator to the maintenance of cell identity, cell cycle regulation and oncogenesis. In the study, we detected EZH2 expression in bladder cancer tissues. These results showed EZH2 high expression in bladder cancer tissue at level of transcript and protein compared with normal bladder tissue and EZH2 expression correlated positively with tumour stage and grade. Then, we used RNA interference to inhibit EZH2 expression in bladder cancer EJ cell line. Efficient downregulation of EZH2 resulted in significantly decreased cell proliferation in EJ cells and retarded transition of G(1) phase to S phase. Our data suggest that EZH2 is involved in the tumourigenesis of bladder cancer and EZH2 downregulation contributes to inhibiting malignant growth by retarding cell entrance to S phase.

Comparison of the molecular adsorbent recirculating system and plasmapheresis for patients with graft dysfunction after liver transplantation

BACKGROUND

Graft dysfunction after liver transplantation (OLT) is a life- threatening condition. Molecular adsorbent recirculating system (MARS) or plasmapheresis (PLP) may be effective supportive therapy of graft dysfunction for patients who cannot undergo retransplantation. The aim of this study was to compare the effects of MARS and PLP in patients with graft dysfunction after OLT.

METHODS

Between January 2002 and July 2007, 31 OLT recipients who experienced graft dysfunction, defined as hyperbilirubinemia (>10 mg/dL) without bile duct obstruction and/or presence of hepatic encephalopathy, were treated with MARS or PLP. Biochemical and hemodynamic data and survival were compared in MARS and PLP groups.

RESULTS

Fifteen patients were treated with 41 MARS sessions and 16 with 105 PLP sessions. After a single MARS session, patients showed significant reductions in creatinine, urea nitrogen, bilirubin, and ammonia. After a single PLP session, patients showed significant improvements in prothrombin time, bilirubin, alanine aminotransferase, alkaline phosphatase, and albumin. After the completion of treatment, Both MARS and PLP significantly improved bilirubin values. at 90 days there were no differences in overall survival rates; 53% in MARS versus 56% in PLP.

CONCLUSION

Both MARS and PLP are alternative supportive treatments for graft dysfunction after OLT.

Lithium rescues the impaired autophagy process in CbCln3(Δex7/8/Δex7/8) cerebellar cells and reduces neuronal vulnerability to cell death via IMPase inhibition

Juvenile neuronal ceroid lipofuscinosis (Batten disease) is a neurodegenerative disorder caused by mutation in CLN3. Defective autophagy and concomitant accumulation of autofluorescence enriched with mitochondrial ATP synthase subunit c were previously discovered in Cln3 mutant knock-in mice. In this study, we show that treatment with lithium reduces numbers of LC3-positive autophagosomes and accumulation of LC3-II in Cln3 mutant knock-in cerebellar cells (CbCln3(Δex7/8/Δex7/8) ). Lithium, an inhibitor of GSK3 and IMPase, reduces the accumulation of mitochondrial ATP synthase subunit c and autofluorescence in CbCln3(Δex7/8/Δex7/8) cells, and mitigates the abnormal subcellular distribution of acidic vesicles in the cells. L690,330, an IMPase inhibitor, is as effective as lithium in restoring autophagy in CbCln3(Δex7/8/Δex7/8) cells. Moreover, lithium or down-regulation of IMPase expression protects CbCln3(Δex7/8/Δex7/8) cells from cell death induced by amino acid deprivation. These results suggest that lithium overcomes the autophagic defect in CbCln3(Δex7/8/Δex7/8) cerebellar cells probably through IMPase, thereby reducing their vulnerability to cell death.

Electro-optic guided-to-radiation mode conversion in annealed proton-exchanged PPLN waveguides

We report the design and experimental demonstration of electro-optically active TM-guided to TE-radiation mode converters in annealed proton-exchanged (APE) periodically poled lithium niobate (PPLN) channel waveguides in telecom S-C-L bands (1495-1640 nm). A maximum mode conversion efficiency of >95%/cm was obtained at 1520 nm from a 24-μm-period APE PPLN waveguide under an electro-optic (EO) field of ~6.3 V/μm at 35°C. This efficiency has been enhanced by a factor of >4.6 over a waveguide built in the single-domain (unpoled) LiNbO3; it is also to the best of our knowledge the most efficient guided-to-radiation (GTR) mode converter ever reported based on LiNbO3 on-axis waveguides. A conversion bandwidth of ~250 nm was also observed from this EO GTR mode converter.

Interrelationship between exposure to PCDD/Fs and hypertension in metabolic syndrome in Taiwanese living near a highly contaminated area

Metabolic syndrome (MetS) consists of a constellation of metabolic abnormalities that confer increased risk of cardiovascular disease. There is a positive correlation between exposure to persistent organic pollutants and MetS. We examine the association between PCDD/Fs and MetS components in 1490 non-diabetic persons living near a highly dioxin-contaminated area. We used factor analysis, with a set of core variables considered central features of MetS and PCDD/Fs, to group similar risk factors. Serum PCDD/Fs were positively and significantly correlated with the number of MetS components. Four risk factors-lipidemia, blood pressure, body size, and glycemia-accounted for 72.6% of the variance in the 10 core factors, and PCDD/Fs were linked to MetS through shared correlations with high blood pressure. After adjusting for confounding factors, we found that diastolic blood pressure (β=0.018; p=0.006), glucose (β=0.013; p=0.046), and waist circumference (β=0.721; p=0.042) significantly increased with increasing serum PCDD/F levels. We found significant trends for associations between metabolic syndrome and serum low-chlorinated PCDD/Fs. The highest quintiles of 2,3,4,7,8-PeCDF, 1,2,3,6,7,8-HxCDF and 2,3,7,8-TCDD had the top three adjusted ORs (95% CI) of 3.5 (1.9-6.3), 2.9 (1.7-4.9) and 2.8 (1.6-4.9), respectively. We also found a slight monotonic relationship between serum PCDD/Fs and the prevalence of MetS, especially when the serum dioxin level was higher than 25.4pg WHO(98)-TEQ(DF)g(-1) lipid (the fourth Quintile). We hypothesize that high-dose exposure to PCDD/Fs is a blood pressure-related factor that raises MetS risk.

Pulsed orange generation optimized in a diode-pumped Nd:YVO4 laser using monolithic dual PPLN electro-optic Q switches

We report a pulsed intracavity sum-frequency generator in a diode-pumped, dual-wavelength Nd:YVO(4) laser whose operation was optimized with two electro-optic Q switches built in a monolithic periodically poled lithium niobate (PPLN) crystal. The dual PPLN Q switches, though integrated, are able to work separately at their respective working wavelengths of 1064 and 1342 nm. At 4.8 W diode pump power and 5 kHz Q-switching rate, a maximum orange (593 nm) output peak power of >480 W was achieved in this laser system using the Q-switch opening-time offset technique. This power is approximately 1.7 times higher than that obtained with the system operated in a conventional single-Q-switch mode.

SCAMP5 links endoplasmic reticulum stress to the accumulation of expanded polyglutamine protein aggregates via endocytosis inhibition

Accumulation of expanded polyglutamine proteins is considered to be a major pathogenic biomarker of Huntington disease. We isolated SCAMP5 as a novel regulator of cellular accumulation of expanded polyglutamine track protein using cell-based aggregation assays. Ectopic expression of SCAMP5 augments the formation of ubiquitin-positive and detergent-resistant aggregates of mutant huntingtin (mtHTT). Expression of SCAMP5 is markedly increased in the striatum of Huntington disease patients and is induced in cultured striatal neurons by endoplasmic reticulum (ER) stress or by mtHTT. The increase of SCAMP5 impairs endocytosis, which in turn enhances mtHTT aggregation. On the contrary, down-regulation of SCAMP5 alleviates ER stress-induced mtHTT aggregation and endocytosis inhibition. Moreover, stereotactic injection into the striatum and intraperitoneal injection of tunicamycin significantly increase mtHTT aggregation in the striatum of R6/2 mice and in the cortex of N171-82Q mice, respectively. Taken together, these results suggest that exposure to ER stress increases SCAMP5 in the striatum, which positively regulates mtHTT aggregation via the endocytosis pathway.

Effect of citral, eugenol, nerolidol and alpha-terpineol on the ultrastructural changes of Trichophyton mentagrophytes

The antifungal effects of citral, eugenol, nerolidol and alpha-terpineol on Trichophyton mentagrophytes were investigated. Citral over 0.1 mg/ml strongly inhibited the hyphal growth of T. mentagrophytes, and the antifungal activity of alpha-terpineol was less effective. The morphological changes of the fungus exposed to the terpenes were observed by electron microscopy. The hyphae were distorted and collapsed at 0.2, 0.4 and 1 mg/ml of eugenol, nerolidol and alpha-terpineol respectively, and cell membrane and organelles were irreversibly damaged at 0.2 mg/ml citral. These suggested that four terpenes possess antifungal activity against T. mentagrophytes, and the activity might lead to irreversible cellular disruption.

Gamma knife radiosurgery for medically refractory idiopathic trigeminal neuralgia

Gamma knife radiosurgery (GKS) has been generally considered as a viable therapeutic option for the management of medically refractory idiopathic trigeminal neuralgia (TN). We reviewed our experience with GKS in patients with TN. Between Feb 1996 and May 2006, 77 patients with medical refractory idiopathic TN were treated using GKS. Thirty-six patients who had undergone other previous procedures, previous GKS, or had brain stem lesion, atypical symptoms, were excluded from this study. Pain improvement was achieved in 38 of the patients with TN (pain response rate 92.7%). Twenty-three patients were pain free and 15 had reduced pain. There were no serious complications. We think that GKS is an effective treatment option for patients with medical refractory idiopathic TN.

Protection of cardiomyocytes from ischemic/hypoxic cell death via Drbp1 and pMe2GlyDH in cardio-specific ARC transgenic mice

The ischemic death of cardiomyocytes is associated in heart disease and heart failure. However, the molecular mechanism underlying ischemic cell death is not well defined. To examine the function of apoptosis repressor with a caspase recruitment domain (ARC) in the ischemic/hypoxic damage of cardiomyocytes, we generated cardio-specific ARC transgenic mice using a mouse alpha-myosin heavy chain promoter. Compared with the control, the hearts of ARC transgenic mice showed a 3-fold overexpression of ARC. Langendoff preparation showed that the hearts isolated from ARC transgenic mice exhibited improved recovery of contractile performance during reperfusion. The cardiomyocytes cultured from neonatal ARC transgenic mice were significantly resistant to hypoxic cell death. Furthermore, the ARC C-terminal calcium-binding domain was as potent to protect cardiomyocytes from hypoxic cell death as ARC. Genome-wide RNA expression profiling uncovered a list of genes whose expression was changed (>2-fold) in ARC transgenic mice. Among them, expressional regulation of developmentally regulated RNA-binding protein 1 (Drbp1) or the dimethylglycine dehydrogenase precursor (pMe(2)GlyDH) affected hypoxic death of cardiomyocytes. These results suggest that ARC may protect cardiomyocytes from hypoxic cell death by regulating its downstream, Drbp1 and pMe(2)GlyDH, shedding new insights into the protection of heart from hypoxic damages.

Current status and issues in cancer stem cell study

Cancer stem cells (CSCs) have been positively identified and successfully isolated from some but not all cancers. The studies on CSCs to date suggest that these cells are rare among the tumor cell population, and they are capable of self-renewing and maintaining tumor growth and heterogeneity. Therapies aimed at CSCs have shown some promise, but their further development will require a more thorough understanding of the biology of CSCs and methods for identifying and isolating this cell subpopulation. This review examines what is known to date regarding the similarities and differences between cancer and somatic stem cells: CSC surface marker development and cell isolation (including a model isolation from our lab), the frequency, potential origin, and signal transduction of CSCs, and the current state of CSC-targeting therapeutic strategies.

Bladder cancer initiating cells (BCICs) are among EMA-CD44v6+ subset: novel methods for isolating undetermined cancer stem (initiating) cells

Bladder cancer stem (initiating) cell has not been isolated now, and no one verified its persistence experimentally. The aim of this study was to conclude the persistence of bladder cancer stem (initiating) cell in human primary bladder cancer and investigate the possibility of EMA(-) CD44v6(+) as markers of bladder cancer stem (initiating) cell. Genes differentially expressed between normal urothelium and low malignant bladder cancer were identified by DNA array assay. Overpressed stem cell related genes, Bmi-1 and EZH2, were verified by immunohistochemistry. Side population cells in bladder cancer were found under fluorescence microscope. The value of 28 potential surface markers of bladder cancer stem (initiating) cell for isolating them were judged by immunohistochemistry. Both EMA(-) and CD44v6(+) cells located in basal layer (potential location of stem cells). After gathering the CD44v6(+) cells and EMA(-) cells by magnetic cell sorting, their ability for colony-forming, self-renewal and extensive proliferation were assayed by cells culture. Both EMA(-) cells and CD44v6(+) cells posses the ability for colony-forming, self-renewal and proliferation. We conclude the persistence of bladder cancer stem (initiating) cell. Bladder cancer stem (initiating) cell might be among EMA(-) CD44v6(+) subset. Our strategies for isolating bladder cancer stem (initiating) cell might be useful for isolating other undetermined epithelial cancer stem cell, especially those in well-differentiated cancers.

AAV-GAD gene for rat models of neuropathic pain and Parkinson's disease

The introduction of therapeutic genes to neurons by genetic modification has potential as an effective treatment for CNS disorders for all that a successful clinical application has not yet been fully implemented. In this paper, we will discussed the role of AAV vectors with the GAD65 gene for animal models of PD and neuropathic pain. AAV vector is one of the most attractive gene delivery vehicles for direct introduction of therapeutic genes into the CNS in the treatment of neurological diseases. GAD65 is present as a membrane-associated form in synapses and is primarily involved in producing synaptic gamma-aminobutyric acid (GABA) for vesicular release. We constructed rAAV-GAD65 expressing rat GAD65 and demonstrated that rat Parkinsonian symptoms can be significantly improved concomitantly with the production of GAD65. We also demonstrated rAAV-GAD65 as a successful gene delivery vehicle in a chronic pain model by administrating rAAV-GAD65 to DRGs because GABA driven by GAD is a major inhibitory neurotransmitter in the dorsal horn of the spinal cord and also plays an important role in the ventral horn. We believe that AAV vectors can be excellent candidates for gene therapy of neurological diseases.

Dopamine transporter density in the basal ganglia in obsessive-compulsive disorder, measured with [123I]IPT SPECT before and after treatment with serotonin reuptake inhibitors

It has been suggested that dopamine as well as serotonin are associated with the pathophysiology of obsessive-compulsive disorder (OCD). 5-Hydroxytryptophan inhibits dopamine release in healthy persons as well as in patients with OCD, and serotonin tonic inhibition affects dopamine function in basal ganglia, indicating a close relationship between serotonin and the dopamine system. Using iodine-123-labeled N-(3-iodopropen-2-yl)-2 beta-carbomethoxy-3beta-(4-chlorophenyl) tropane ([(123)I]IPT) single photon emission computed tomography (SPECT), we investigated the dopamine transporter (DAT) density in the basal ganglia of patients with OCD. The test consists of two measurements before and after treatment with serotonin reuptake inhibitors (SRIs). Ten patients with OCD before and after treatment with SRIs were included. We performed brain SPECT 2 h after intravenous administration of [(123)I]IPT using a dual-head SPECT camera (Vertex, ADAC, Calif., USA) and analyzed the SPECT data, reconstructed for the assessment of the specific/nonspecific DAT binding ratio in the basal ganglia. We then examined the correlation between the scores of OCD symptom changes, assessed with the Yale-Brown Obsessive-Compulsive Scale (Y-BOCS), and DAT binding ratio. Patients with OCD after treatment with SRIs showed a significantly decreased DAT binding ratio in the right basal ganglia compared with baseline. A significant correlation was found between the total scores and compulsion score changes of the Y-BOCS and the changes of the DAT binding ratio of the right basal ganglia. These findings suggest that the dopaminergic neurotransmitter system of the basal ganglia could play an important role in the symptom improvement of OCD patients.

Infantile spasm-associated microencephaly in tuberous sclerosis complex and cortical dysplasia

OBJECTIVE

In children with and without infantile spasms, this study determined brain volumes and cell densities in epilepsy surgery patients with tuberous sclerosis complex (TSC) and cortical dysplasia with balloon cells (CD).

METHODS

We compared TSC (n = 18) and CD (n = 17) patients with normal/autopsy controls (n = 20) for MRI gray and white matter volumes and neuronal nuclei (NeuN) cell densities.

RESULTS

In patients without a history of infantile spasms, TSC cases showed decreased gray and white matter volumes (-16%). In cases with a history of infantile spasms, both CD (-25%) and TSC (-35%) patients showed microencephaly. This was confirmed in monozygotic twins with TSC, where the twin with a history of spasms had cerebral volumes less (-16%) than the twin without a history of seizures. Regardless of seizure history, TSC patients showed decreased NeuN cell densities in lower gray matter (-36%), whereas CD patients had increased densities in upper cortical (+52%) and white matter regions (+65%). For TSC patients, decreased lower gray matter NeuN densities correlated with reduced MRI volumes.

CONCLUSIONS

Patients with tuberous sclerosis without spasms showed microencephaly associated with decreased cortical neuronal densities. In contrast, cortical dysplasia patients without spasms were normocephalic with increased cell densities. This supports the concept that tuberous sclerosis and cortical dysplasia have different pathogenetic mechanisms despite similarities in refractory epilepsy and postnatal histopathology. Furthermore, a history of infantile spasms was associated with reduced cerebral volumes in both cortical dysplasia and tuberous sclerosis patients, suggesting that spasms or their treatment may contribute to microencephaly independent of etiology.

Neuronal vulnerability of CLN3 deletion to calcium-induced cytotoxicity is mediated by calsenilin

Calsenilin/DREAM/KChIP3, a neuronal Ca(2+)-binding protein, has multifunctions in nucleus and cytosol. Here, we identified CLN3 as a calsenilin-binding partner whose mutation or deletion is observed in Batten disease. In vitro binding and immunoprecipitation assays show that calsenilin interacts with the C-terminal region of CLN3 and the increase of Ca(2+) concentration in vitro and in cells causes significant dissociation of calsenilin from CLN3. Ectopic expression of CLN3 or its deletion mutant containing only the C-terminus (153-438) and capable of binding to calsenilin suppresses thapsigargin or A23187-induced death of neuronal cells. In contrast, CLN3 deletion mutant containing the N-terminus (1-153) or (1-263), which is frequently found in Batten disease, induces the perturbation of Ca(2+) transient and fails to inhibit the cell death. In addition, the expression of calsenilin is increased in the brain tissues of CLN3 knock-out mice and SH-SY5Y/CLN3 knock-down cells. Down-regulation of CLN3 expression sensitizes SH-SY5Y cells to thapsigargin or A23187. However, additional decrease of calsenilin expression rescues the sensitivity of SH-SY5Y/CLN3 knock-down cells to Ca(2+)-mediated cell death. These results suggest that the vulnerability of CLN3 knock-out or CLN3 deletion (1-153)-expressing neuronal cells to Ca(2+)-induced cell death may be mediated by calsenilin.

Enhanced expression of glutamate decarboxylase 65 improves symptoms of rat parkinsonian models

In this study, we report the amelioration of parkinsonian symptoms in rat Parkinson's disease (PD) models, as a result of the expression of glutamate decarboxylase (GAD) 65 with a modified cytomegalovirus (CMV) promoter. The transfer of the gene for gamma-amino butryic acid (GAD), the rate-limiting enzyme in gama-amino butrylic acid (GABA) production, has been investigated as a means to increase inhibitory synaptic activity. Electrophysiological evidence suggests that the transfer of the GAD65 gene to the subthalamic nucleus (STN) can change the excitatory output of this nucleus to inhibitory output. Our in vitro results also demonstrated higher GAD65 expression in cells transfected with the JDK promoter, as compared to cells transfected with the CMV promoter. Also, a rat PD model in which recombinant adeno-associated virus-2 (rAAV2)-JDK-GAD65 was delivered into the STN exhibited significant behavioral improvements, as compared to the saline-injected group. Interestingly, we observed that these behavioral improvements were more obvious in rat PD models in which rAAV2-JDK-GAD65 was injected into the STN than in rat PD models in which rAAV2-CMV-GAD65 was injected into the STN. Moreover, according to electrophysiological data, the rAAV2-JDK-GAD65-injected group exhibited more constant improvements in firing rates than did the rAAV2-CMV-GAD65-injected group. These data indicate that the JDK promoter, when coupled with GAD65 expression, is more effective with regard to parkinsonian symptoms than is the CMV promoter.

Differential gene expression profiling in aggressive bladder transitional cell carcinoma compared to the adjacent microscopically normal urothelium by microdissection-SMART cDNA PCR-SSH

Identifying novel and known genes that are differentially expressed in aggressive bladder transitional cell carcinoma (BTCC) has important implications in understanding the biology of bladder tumorigenesis and developing new diagnostic and therapeutic agents. In this study we identified the differential gene expression profiles comparing tumor to the adjacent microscopically normal mucosa by manual microdissection on frozen sections. The RNAs extracted from microdissected tissues were amplified by SMART cDNA PCR technology to generate forward subtractive cDNA library by suppressive subtractive hybridization (SSH). We obtained 376 positive clones, one hundred clones of aggressive BTCC subtracted cDNA library were selected at random and inserts were reamplified by PCR. After differential screening by reverse dot blotting, 73 positive clones, that contend inserts putatively upregulated in aggressive BTCC, were further analysed by DNA sequencing, GenBank and EST database searching. Sequencing results showed that 66 clones stand for 23 known genes and 7 clones for three new EST (Genbank number: DN236875, DN236874 and DN236873). In conclusion, microdissection-SMART cDNA PCR-SSH allowed for an efficient way to identify aggressive BTCC-specific differential expressed genes that may potentially be involved in the carcinogenesis and/or progression of aggressive BTCC. These differentially expressed genes may be of potential utility as therapeutic and diagnostic targets for aggressive BTCC.

Prevention of uncuffed hemodialysis catheter-related bacteremia using an antibiotic lock technique: A prospective, randomized clinical trial

As a result of the high rate of infection, the NKF-K/DOQI guidelines recommended that an uncuffed catheter (UC) should not be used for longer than three weeks. However, the findings of the Dialysis Outcomes and Practice Patterns Study recognized that 48% of new hemodialysis patients in the US and 75% in Europe used UC for temporary access during arteriovenous fistula or graft maturation. The antibiotic lock technique (ALT) has been recommended to prevent catheter-related bacteremia (CRB). Here, we prospectively evaluated the efficacy of catheter-restricted filling using an antibiotic lock solution in preventing CRB. A total of 120 new hemodialysis patients requiring a temporary catheter while waiting for placement and maturation of an arteriovenous fistula or graft were enrolled in this study. Patients with a UC were randomly assigned to receive either an antibiotic-heparin lock solution (antibiotic group: cefazolin 10 mg/ml, gentamicin 5 mg/ml, heparin 1000 U/ml) or a heparin lock solution (no-antibiotic group: heparin 1000 U/ml) as a catheter lock solution during the interdialytic period. The end point of the trial was CRB. CRB developed in seven (11.7%) patients in the no-antibiotic group (Staphylococcus aureus, two; Staphylococcus epidermidis, five) whereas only one patient in the antibiotic group had S. aureus bacteremia. CRB rates per 1000 catheter-days were 0.44 in the antibiotic group versus 3.12 in the no-antibiotic group (P=0.031). Kaplan-Meier analysis also showed that mean CRB-free catheter survival of 59 days (95% CI, 58-61 days) in the antibiotic group was greater than that in the no-antibiotic group (55 days; 95% CI, 50-59 days). The results suggest that ALT may be a beneficial means of reducing the CRB rate in hemodialysis patients with UC.

The behavioral effect of human mesenchymal stem cell transplantation in cold brain injured rats

We investigated the effect of stereotaxically transplanted human mesenchymal stem cells (hMSCs) on behavioral change after traumatic cold brain injury in adult rats. Cortical lesions (n= 20) were induced by touching a metal stamp, cooled with liquid nitrogen, to the dura over the forelimb motor cortex of adult rats. The procedure produced a localized lesion, and the animals showed significant motor deficits. hMSCs were freshly isolated from human iliac bone and cultured in tissue culture flasks with 10 ml Dulbecco's modified Eagle's medium. The animals received hMSC grafts (3 x 10(5) hMSCs) 6 days after cold lesion (n = 10). All rats were sacrificed 3 or 7 weeks after cold injury, and immunohistochemical staining was performed on brain sections to identify donor hMSCs. Neurological evaluations were performed with the forepaw adjusting step test and modified neurological scoring. Treatment with 3 x 10(5) hMSCs improved the rat's neurological functions. We also found that the transplanted cells successfully migrated into the injured brain, preferentially localized around the injury site, and expressed the neuronal and astrocyte marker. These data suggest that hMSCs may be a potential therapeutic tool for brain injuries.

Electrical stimulation of the anterior cingulate cortex in a rat neuropathic pain model

BACKGROUND

Electrical stimulation is currently employed to treat several neurological conditions, including pain and Parkinson's disease. It is one of several minimally invasive alternatives to drug treatments for painful conditions. A number of studies have shown that the anterior cingulate cortex (ACC) plays an important role in the processing of pain and pain modulation. The purpose of this study is to investigate these neuropathic pain-relieving effects by delivering electrical stimulation into the ACC of rat models.

METHODS

Following the approval of the AAALAC and the Guidelines and Regulations for Use and Care of Animals in Yonsei University, rats were subjected to surgery under pentobarbital anesthesia (50 mg/kg, i.p.) to produce neuropathic pain. Electrodes were bilaterally implanted into the ACC with a metal holder for the electrical stimulation. The effect of the electrical stimulation of the ACC on the rat neuropathic pain model was measured by the von Frey test.

FINDINGS

The effect of electrical stimulation of the ACC on neuropathic pain was shown during stimulation at 30, 40, 50, and 60 min, and at 10 min after stimulation. In the pain ACC stimulation group, the response of mechanical allodynia was significantly reduced during the time of ACC electrical stimulation.

CONCLUSION

The mechanical allodynia of the neuropathic pain could be modulated by ACC electrical stimulation.

Molecular pathology of low malignant bladder transitional cell carcinoma: a current perspective

Bladder transitional cell carcinoma (BTCC) actually has two phenotypes: low malignant and aggressive. Most previous molecular and cytogenetic analyses of bladder cancer were focused on aggressive BTCC. Little is known about the events that lead to the development of low malignant BTCC. This review mainly introduces the concept of two types of bladder tumors and then focuses on the molecular pathology of low malignant BTCC in particular. It is hoped that further understanding of the molecular pathology of low malignant BTCC may provide novel therapies and many other clinical benefits in patients with this disease.

Calcium binding of ARC mediates regulation of caspase 8 and cell death

Apoptosis repressor with CARD (ARC) possesses the ability not only to block activation of caspase 8 but to modulate caspase-independent mitochondrial events associated with cell death. However, it is not known how ARC modulates both caspase-dependent and caspase-independent cell death. Here, we report that ARC is a Ca(2+)-dependent regulator of caspase 8 and cell death. We found that in Ca(2+) overlay and Stains-all assays, ARC protein bound to Ca(2+) through the C-terminal proline/glutamate-rich (P/E-rich) domain. ARC expression reduced not only cytosolic Ca(2+) transients but also cytotoxic effects of thapsigargin, A23187, and ionomycin, for which the Ca(2+)-binding domain of ARC was indispensable. Conversely, direct interference of endogenous ARC synthesis by targeting ARC enhanced such Ca(2+)-mediated cell death. In addition, binding and immunoprecipitation analyses revealed that the protein-protein interaction between ARC and caspase 8 was decreased by the increase of Ca(2+) concentration in vitro and by the treatment of HEK293 cells with thapsigargin in vivo. Caspase 8 activation was also required for the thapsigargin-induced cell death and suppressed by the ectopic expression of ARC. These results suggest that calcium binding mediates regulation of caspase 8 and cell death by ARC.