Deep sequencing of small RNA libraries reveals dynamic expression patterns of microRNAs in multiple developmental stages of Bactrocera dorsalis

In eukaryotes, microRNAs (miRNAs) are small, conserved, noncoding RNAs that have emerged as critical regulators of gene expression. The oriental fruit fly Bactrocera dorsalis is one of the most economically important fruit fly pests in East Asia and the Pacific. Although transcriptome analyses have greatly enriched our knowledge of its structural genes, little is known about post-transcriptional regulation by miRNAs in this dipteran species. In this study, small RNA libraries corresponding to four B. dorsalis developmental stages (eggs, larvae, pupae and adults) were constructed and sequenced. Approximately 30.7 million reads of 18-30 nucleotides were obtained, with 123 known miRNAs and 60 novel miRNAs identified amongst these libraries. More than half of the miRNAs were stage-specific during the four developmental stages. A set of miRNAs was found to be up- or down-regulated during development by comparison of their reads at different developmental stages. Moreover, a small part of miRNAs owned both miR-#-3p and miR-#-5p types, with enormously variable miR-#-3p/miR-#-5p ratios in the same library and amongst different developmental stages for each miRNA. Taking these findings together, the current study has uncovered a number of miRNAs and provided insights into their possible involvement in developmental regulation by expression profiling of miRNAs. Further analyses of the expression and function of these miRNAs could increase our understanding of regulatory networks in this insect and lead to novel approaches for its control.

Genetic variations of ISL1 associated with human congenital heart disease in Chinese Han people

Congenital heart disease (CHD) is the most common birth abnormality, but the etiology of CHD is unknown. ISL1 may play a fundamental role in cardiac morphogenesis, and mutations of this gene could cause CHD. To evaluate whether genetic variations of ISL1 are associated with CHD in Chinese Han people, polymerase chain reaction restriction fragment-length polymorphism and SNaPshot were used to examine 9 polymorphisms of ISL1 in 233 patients with CHD as well as 288 healthy controls. We found that one SNP (rs1017) in ISL1 was significantly associated with simple CHD. Genetic variation of ISL1 was confirmed to be associated with the risk of CHD. ISL1 is related to the atrial septal defect group and the ventricular septal defect group, and the genotypes were associated with the occurrence of CHD in the dominant mode of inheritance. We concluded that rs1017 contributed to the risk of CHD in Chinese Han people, and ISL1 may be involved in the formation and development of the heart.

Lack of Epstein-Barr virus infection in Chinese myasthenia gravis patients

OBJECTIVE

There are three recent contradictory reports on the incidence of Epstein-Barr virus in the pathogenesis of myasthenia gravis, with all studies carried out in Caucasian patients. The current study evaluated whether Epstein-Barr virus infection had a role in the pathogenesis of myasthenia gravis in a cohort of 30 Chinese patients.

MATERIALS AND METHODS

Serial paraffin sections of thymic hyperplasia obtained from myasthenia gravis patients were analyzed for the presence of Epstein-Barr virus-encoded small RNA -1 and Epstein-Barr virus latent membrane protein 1 by in situ hybridization and immunohistochemistry, respectively. Epstein-Barr virus(+) cervical lymph nodes from lymphoma patients and Epstein-Barr virus(-) thymus specimens obtained during cardiac surgery served as the positive and negative control groups, respectively.

RESULTS

All the 30 myasthenia gravis specimens were negative for both Epstein-Barr virus-encoded small RNA -1 and Epstein-Barr virus latent membrane protein 1 tests. However, we obtained well-characterized membrane and cytoplasmic immunohistochemical and in situ hybridization staining for both Epstein-Barr virus latent membrane protein 1 and Epstein-Barr virus-encoded small RNA -1, respectively, in the positive control samples.

CONCLUSIONS

Our results therefore do not support a role of thymic Epstein-Barr virus infection in myasthenia gravis pathogenesis and calls for an integration of methodological and interpretation issues in detecting Epstein-Barr virus incidence in myasthenia gravis patients.

Slow and stored light by photo-isomerization induced transparency in dye doped chiral nematics

Decelerating and stopping light is fundamental for optical processing, high performance sensor technologies and digital signal treatment, many of these applications relying on the ability of controlling the amplitude and phase of coherent light pulses. In this context, slow-light has been achieved by various methods, as coupling light into resonant media, Brillouin scattering in optical fibers, beam coupling in photorefractive and liquid crystal media or engineered dispersion in photonic crystals. Here, we present a different mechanism for slowing and storing light, which is based on photo-isomerization induced transparency of azo-dye molecules hosted in a chiral liquid crystal structure. Sharp spectral features of the medium absorption/dispersion, and the long population lifetime of the dye metastable state, enable the storage of light pulses with a significant retrieval after times much longer than the medium response time.

Rare case of cerebral MALToma presenting with stroke-like symptoms and seizures

Mucosa-associated lymphoid tissue (MALT) cells are present in gastrointestinal mucosa but rarely found in the central nervous system (CNS). We describe an unusual and rare case of CNS MALT lymphoma in a patient presenting with stroke-like symptoms.

Phase conjugation and slow light in dye-doped chiral nematics

Optical phase conjugation and slow light are obtained in dye-doped chiral nematics via degenerate four-wave mixing. The creation of the light-induced dynamical grating is described and the amplitude of the phase-conjugate wave is shown to follow the changes of the input signal, hence providing efficient distortion correction. Associated to these capabilities, slowing down of light pulses is obtained thanks to the dispersive properties of the wave mixing occurring in the cholesteric liquid crystals, opening the way to applications in interferometry and imaging through highly scattering media.

SP600125, a JNK inhibitor, suppresses growth of JNK-inactive glioblastoma cells through cell-cycle G2/M phase arrest

SP600125 is a well studied inhibitor of c-Jun N-terminal kinase (JNK). Its direct biochemical effects on JNK-inactive tumor cells are usually ignored. In this study, we investigated the effects of SP600125 on JNK-inactive U251 human glioblastoma cells. Our results demonstrate that, 20 microM or more SP600125 can induce significant cell growth inhibition and cell-cycle G2/M phase arrest in U251 cells. Interestingly, we also found that SP600125 can stop the duplicated chromosomes from separating into two cells and the karyokinesis progression. Our study opened up a new perspective for further studies involved in JNK inhibitors or anti-glioma therapy.

Effectiveness and safety assessment of lamotrigine monotherapy for treatment of epilepsy

BACKGROUND

Epilepsy is a recurrent chronic nervous system disease. A correct choice of antiepileptic drug is the key to control seizures and improve patient's life quality.

AIM

To study the effectiveness and safety of lamotrigine monotherapy for treatment of epilepsy, systemic evaluation was carried out on published comparative trials between lamotrigine and carbamazepine.

METHODS

The retrieval method referred to the search strategy developed by Cochrane Epilepsy Group and software Rev.Man 5 was used for META analysis and forest plots. The Odds ratio (OR) was selected as the effect size and funnel plot was used to analyze the publication bias.

RESULTS

A total of 9 studies and 2269 cases of patients were included in the analysis. There was no significant difference between lamotrigine and carbamazepine for treatment of epilepsy as the OR was 1.17, 95% confidence interval (CI) [0.88, 1.54]. However, lamotrigine had advantages in the overall withdrawal rate and withdrawal rate due to side effects as the ORs were 0.57, 95% CI [0.47, 0.69] and 0.41, 95% CI [0.32, 0.52].

CONCLUSIONS

Lamotrigine has certain advantages over carbamazepine for treatment of epilepsy as it has less side effects and higher tolerability. In addition, the quality of such clinical trials should be further improved to have a more comprehensive understanding.

T helper type 17 cells expand in patients with myasthenia-associated thymoma

Myasthenia gravis (MG) is a prototypical CD4(+) T cell-dependent autoimmune disease mediated by anti-acetylcholine receptor autoantibodies (AChR-Abs). Certain subsets of helper T cells are suggested to be involved in the pathogenesis of MG, including Th1 and regulatory T cells (Treg). However, whether the recently identified Th17 cells play a role in the development of MG and its prognosis is still unknown. Here, we demonstrated that Th17 cells and their associated cytokines are increased, while the Treg cells are decreased in the peripheral blood mononuclear cells (PBMCs) from MG patients with thymomas (TM), but not from those with normal thymus (NT) or thymic hyperplasia (TH). Furthermore, the quantity of Th17 cells correlates with the quantitative myasthenia gravis (QMG) score in patients with TM. We also found a significant positive relationship between the frequency of Th17 cells (%) and the concentration of AChR antibodies in patients with MG. Therefore, the Th17/Treg imbalance in TM may suggest MG with certain pathological subtype, and the increase in Th17 cells may reveal the severity of the disease, which is valuable in the diagnosis and choice of therapeutic strategy for patients with MG.

Two-wave mixing in chiral dye-doped nematic liquid crystals

Two-wave mixing in nematic liquid crystals doped with dyes and chiral agents is studied. The photo-induced spatial modulation of the chiral structure, together with the diffusion anisotropy of the mixture, determine a relatively fast response time, a spatial resolution of 1 μm, and a maximum gain for circularly polarized interacting beams. The gain is insensitive to changes in linear polarization, while it varies with the grating period and with the pump-to-signal intensity ratio.

Separation of EEG and ECG components based on wavelet shrinkage and variable cosine window

During ambulatory monitoring, it is sometimes required to record an electroencephalogram (EEG) and an electrocardiogram (ECG) simultaneously. It would be ideal if both EEG and ECG could be obtained with one measurement. Here, we introduce an algorithm that combines the wavelet shrinkage and variable cosine window operation to separate the EEG and ECG components from an EEG signal recorded with a noncephalic reference (NCR). Evaluation using simulated data and actual measured data showed that accurate frequency analysis of EEG and an R-R detection-based heart rate analysis were feasible with our proposed algorithm, which improved the signal-averaging based algorithm so that ECG components containing ectopic beats can be applied.

Assessment of mental fatigue during car driving by using high resolution EEG activity and neurophysiologic indices

Driving tasks are vulnerable to the effects of sleep deprivation and mental fatigue, diminishing driver's ability to respond effectively to unusual or emergent situations. Physiological and brain activity analysis could help to understand how to provide useful feedback and alert signals to the drivers for avoiding car accidents. In this study we analyze the insurgence of mental fatigue or drowsiness during car driving in a simulated environment by using high resolution EEG techniques as well as neurophysiologic variables such as heart rate (HR) and eye blinks rate (EBR). Results suggest that it is possible to introduce a EEG-based cerebral workload index that it is sensitive to the mental efforts of the driver during drive tasks of different levels of difficulty. Workload index was based on the estimation of increase of EEG power spectra in the theta band over prefrontal areas and the simultaneous decrease of EEG power spectra over parietal areas in alpha band during difficult drive conditions. Such index could be used in a future to assess on-line the mental state of the driver during the drive task.

Tranilast prevents the progression of chronic cyclosporine nephrotoxicity through regulation of transforming growth factor β/Smad pathways

PURPOSE

Our aim was to investigate the role of tranilast in transforming growth factor (TGF) β/Smad pathways using a rat model of chronic cyclosporine (CsA) nephrotoxicity.

METHODS

Thirty Sprague-Dawley (SD) rats were equally randomized in to 5 groups for gavage treatments daily for 4 weeks: normal control (N), olive oil; CsA (25 mg/kg), (M) CsA plus low-dose tranilast group (T1; CsA 25 mg/kg and tranilast 100 mg/kg); CsA plus medium-dose tranilast group (T2; CsA 25 mg/kg and tranilast 200 mg/kg); and CsA plus high-dose tranilast group (T4; CsA 25 mg/kg and tranilast 400 mg/kg). Kidneys were harvested at the end of the fourth week. TGF-β1 as well as Smad3 and Smad7 were detected by reverse-transcription polymerase chain reaction and immunohistochemistry.

RESULTS

The administration of tranilast decreased the expression of TGF-β1 and Smad3 by CsA-treated rats, whereas it increased both mRNA and protein levels of Smad7. Semiquantitative analysis of mRNA production revealed these treatments to markedly reduce the amount of TGF-β1: T1: 0.8452 ± 0.0825 vs 0.8529 ± 0.0606 (P < .05); T2: 0.8414 ± 0.0696 vs 0.8529 ± 0.0606 (P < .05); T4: 0.8336 ± 0.0592 vs 0.8529 ± 0.0606 (P < .05). For Smad3: T1: 0.8581 ± 0.0328 vs 0.8613 ± 0.0542 (P < .05); T2: 0.8528 ± 0.0599 vs 0.8613 ± 0.0542 (P < .05); T4: 0.8436 ± 0.0185 vs 0.8613 ± 0.0542 (P < .05). The significantly elevated dose-dependent amounts of Smad7 were: T1: 0.9026 ± 0.0522 vs 0.8678 ± 0.0246, (P < .05); T2: 0.9087 ± 0.0506 vs 0.8678 ± 0.0246 (P < .05); T4: 0.9151 ± 0.0793 vs 0.8678 ± 0.0246 (P < .05).

CONCLUSION

Regulation of TGF-β/Smad pathways is one of the mechanisims by which tranilast mitigates the progression of chronic CsA nephrotoxicity in rats.

A prospective randomized study comparing open versus laparoscopy-assisted D2 radical gastrectomy in advanced gastric cancer

BACKGROUND

In recent years, many clinical studies have confirmed the value of laparoscopy-assisted gastrectomy (LAG) in gastric cancer surgery, especially in early stages. But the safety and oncologic adequacy of laparoscopy-assisted D2 radical gastrectomy for advanced gastric cancer are still in debate. We conducted a prospective randomized trial to compare open versus laparoscopy-assisted D2 radical gastrectomy in advanced gastric cancer.

METHODS

For this study, 123 patients who had been diagnosed endoscopically with gastric cancer were randomly assigned to either LAG (n = 61) or open gastrectomy (OG) (n = 62) which ran from March 2008 to December 2009. Clinical characteristics, operative findings, postoperative recovery, morbidity, pathological report and survival rate were compared. D2 lymph node dissection was performed in 49 patients in the LAG group and 47 patients in the OG group with advanced gastric cancer. We adopt sub-group analysis in this paper.

RESULTS

The clinical characteristics of patients in the LAG and OG groups who were in the advanced stage, included age, sex, BMI and concurrent illness, and their ECOG scores were well matched. Operative findings, postoperative recovery, morbidity, pathological findings including tumor location, depth of invasion, TNM stage, histological grade and surgical extension in the two groups were also similar. Compared to the OG group, the mean operating time was significantly longer for the LAG group (267.88 ± 54.284 min in the LAG group vs. 182.02 ± 41.016 min in the OG group, p = 6.383 × 10(-13)); the mean number of days when body temperature exceeded 37°C was significantly shorter in the LAG group (p = 6.34 × 10(-8)). There were no postoperative deaths in both the groups. The postoperative morbidity rate was 12.24% in the LAG group and 19.15% in the OG group with no significant difference (p = 0.357). However, pulmonary infection was observed more frequently in the OG group (p = 0.038). After a mean follow-up of 22.1354 months (from 4 to 36 months), 14 and 15 patients died of gastric cancer in the LAG and OG groups, respectively. Two and one patient died of nongastric cancer in the LAG and OG groups, respectively. The overall survival rates were 67.1% and 53.8% in the LAG and OG groups, respectively. The estimated mean survival time was 29.387 months in the LAG group and 28.978 months in the OG group. There was no statistically significant difference in the overall survival rate for patients in both groups - LAG and OG (log-rank test, p = 0.911, Tarone Ware test, p = 0.994, and Breslow test, p = 0. 961).

CONCLUSION

LAG with D2 lymph node dissection is a safe and feasible procedure with adequate lymphadenectomy, good curability and survival rate for the treatment of advanced gastric cancer.

RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences

MOTIVATION

RNA secondary structure plays an important role in the function of many RNAs, and structural features are often key to their interaction with other cellular components. Thus, there has been considerable interest in the prediction of secondary structures for RNA families. In this article, we present a new global structural alignment algorithm, RNAG, to predict consensus secondary structures for unaligned sequences. It uses a blocked Gibbs sampling algorithm, which has a theoretical advantage in convergence time. This algorithm iteratively samples from the conditional probability distributions P(Structure | Alignment) and P(Alignment | Structure). Not surprisingly, there is considerable uncertainly in the high-dimensional space of this difficult problem, which has so far received limited attention in this field. We show how the samples drawn from this algorithm can be used to more fully characterize the posterior space and to assess the uncertainty of predictions.

RESULTS

Our analysis of three publically available datasets showed a substantial improvement in RNA structure prediction by RNAG over extant prediction methods. Additionally, our analysis of 17 RNA families showed that the RNAG sampled structures were generally compact around their ensemble centroids, and at least 11 families had at least two well-separated clusters of predicted structures. In general, the distance between a reference structure and our predicted structure was large relative to the variation among structures within an ensemble.

AVAILABILITY

The Perl implementation of the RNAG algorithm and the data necessary to reproduce the results described in Sections 3.1 and 3.2 are available at http://ccmbweb.ccv.brown.edu/rnag.html

CONTACT

charles_lawrence@brown.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.