Genomic survey and gene expression analysis of the VDAC gene family in rice

The voltage-dependent anion channel (VDAC), also known as a mitochondrial porin, plays an important role in the regulation of metabolic and energetic functions of mitochondria, as well as in mitochondria-mediated apoptosis. Cytoplasmic male sterility (CMS) is of major economic importance for commercial hybrid production and a research model for the interaction be-tween nuclear and cytoplasmic genomes. Recent research has revealed that CMS is associated with programmed cell death. Here, we used the Honglian (HL)-CMS line of rice (Oryza sativa) as material to investigate the association of O. sativa VDAC (OsVDAC) expression to CMS. Eight VDACs were extracted from rice in this study. Bioinformatic analysis of the rice VDACs was conducted at the DNA, cDNA, and protein level. Expression patterns of OsVDACs were analyzed in different organs and during different stages of pollen development using sterile line YuetaiA (YTA), and its maintainer line YuetaiB (YTB). Differential expression of OsVDACs between YTA and YTB was observed, suggesting that VDACs may be involved in the formation of HL-CMS.

Abstract B56: An immuno-gene therapy clinical trial evaluating in situ vaccination of malignant pleural mesothelioma with intrapleural delivery of adenovirus-interferon-alpha-2b in combination with chemotherapy

Background: “In situ vaccination” immune-gene therapy has the ability to induce broad, polyclonal anti-tumor responses directed by the patient's own immune system using standard “off the shelf” agents. In this trial, we activated endogenous tumor immunity by injection of an adenovirus expressing a Type I interferon into the pleural space of patients with malignant pleural mesothelioma (MM). Based on preclinical data showing synergy with chemotherapy, all patients then received standard systemic cytotoxic therapy.

Methods: Two doses of intrapleural administration of a replication-defective recombinant adenoviral vector containing the human interferon-alpha (hIFN-α2b) gene at a dose of 3x1011 viral particles were given concomitant with a 14-day course of high-dose cyclo-oxygenase-2 (COX-2) inhibitor (Celecoxib) to reduce side effects and to modify the tumor microenvironment by decreasing PGE- 2 levels. This was followed by standard first-line or second-line chemotherapy agents. Primary outcome measures were safety, overall best response rate, and survival. Bio-correlates were measured.

Results: Forty patients were treated in this study: 18 patients received first-line Pemetrexed-based chemotherapy; 7 patients who had previously received front-line Pemetrexed-based chemotherapy >6 months prior to enrollment received Pemetrexed-based second-line chemotherapy. Additionally, in the second-line chemotherapy arm, fifteen patients (n=15) received gemcitabine-based chemotherapy. Treatment was well tolerated and adverse events were comparable to historical controls. Follow-up chest CT scans demonstrated an overall response rate of 20% by Modified RECIST criteria and disease control rate (DCR) of 85% (partial and complete responses plus stable disease) at initial follow-up scan after the first two cycles of chemotherapy. Encouragingly, median survival for all patients with epithelial histology (including both first and second line) was 26 months (95% CI: 15-ND); median overall survival (MOS) for patients with non-epithelial histology (both first and second line) was 6.5 months (95% CI: 5.50 – ND). [See figure] Historical MOS with first line chemotherapy alone is 13.3 months. No clear predictors for response were identified including: baseline immunologic parameters (i.e. activated T cells or number of regulatory T cells); the presence of the immune-gene signature in their biopsies; peak levels of interferon in blood or pleural fluid; or induction of anti-tumor antibodies, activated T cells, or natural killer cells in peripheral blood.

Conclusions: The combination of intrapleural Ad.IFN-α2b vector, Celecoxib, and systemic chemotherapy proved safe in patients with unresectable malignant pleural mesothelioma. Overall survival rates were significantly higher than historical controls, particularly in the second-line groups. The results of this study support proceeding with a multi-center randomized clinical trial of chemo-immunogene therapy versus standard chemotherapy alone.

Citation Format: D. H. Sterman, E. Alley, J. Friedberg, S. Metzger, J. Stevenson, E. Moon, A. R. Haas, A. Vachani, S. I. Katz, G. Cheng, J. Sun, D. F. Heitjan, L. Litzky, K. Cengel, C. B. Simone, II, M. Culligan, M. Culligan, S. M. Albelda. An immuno-gene therapy clinical trial evaluating in situ vaccination of malignant pleural mesothelioma with intrapleural delivery of adenovirus-interferon-alpha-2b in combination with chemotherapy. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr B56.

Duration of day care attendance during infancy predicts asthma at the age of seven: the Cincinnati Childhood Allergy and Air Pollution Study

BACKGROUND

Studies vary with respect to the reported effects of day care attendance on childhood asthma.

OBJECTIVES

To evaluate the independent and combined effects of day care attendance and respiratory infections on the development of asthma at the age of seven in a prospective birth cohort.

METHOD

At the age of seven, the study sample included 589 children with complete data of 762 enrolled at birth. Day care hours and number of respiratory infections were reported in follow-up questionnaires through age four. At 7 years of age, asthma was diagnosed in 95 children (16%), based on predefined symptoms criteria confirmed by either asthma FEV1 reversibility after bronchodilator or a positive methacholine test (PC20 ≤ 4 mg/mL). Logistic regression was used to investigate the relationships between asthma at the age of seven, cumulative hours of day care attendance and reported respiratory infections at ages 1-4.

RESULTS

In the univariate analyses, day care attendance at 12 months was associated with an increased risk of asthma [odds ratio (OR) = 1.8, 95% confidence interval (CI) = 1.1-3.0]. Both upper and lower respiratory infections at 12 months also increased the likelihood of asthma [OR = 2.4 (1.4-4.1); OR = 2.3 (1.5-3.7), respectively]. In the final multivariate logistic model, cumulative hours of day care attendance and number of lower respiratory infections at 12 months were associated with asthma [OR = 1.2 (1.1-1.5); OR = 1.4 (1.2-1.7), respectively]. However, a threshold of greater than 37.5 hours per week of day care attendance was associated with a lower risk of asthma [OR = 0.6 (0.4-0.9)].

CONCLUSION

Depending on duration of attendance, day care during infancy can either increase or reduce risk of asthma at the age of seven.

Identification of Campylobacter jejuni and determination of point mutations associated with macrolide resistance using a multiplex TaqMan MGB real-time PCR

AIMS

The aim of the study was to develop a multiplex real-time PCR method to identify Campylobacter jejuni containing mutations commonly associated with macrolide resistance.

METHODS AND RESULTS

A multiplex fluorescence real-time PCR assay was developed based on TaqMan minor groove binder (MGB) probes. The VS1-MGB probe was designed based on the VS1 gene and was used to identify Camp. jejuni. The 23S rDNA-MGB probe was designed to distinguish macrolide resistance mutations in 23S rDNA, while 57D-MGB and 74D-MGB were designed to detect resistance mutations in ribosomal protein L4. The specificity and accuracy of our method were identical to the conventional biochemical tests, mapA PCR, minimum inhibitory concentration (MIC) determination and DNA sequencing. The linear detection limit of the method was 0·03 ng genomic DNA and three colony formation unit (CFU) per reaction. In 6 of 18 cases, the nature of Erythromycin resistance could be correctly determined from natural isolates; absence of the tested mutations was demonstrated in the remaining four resistant isolates.

CONCLUSIONS

A multiplex TaqMan MGB real-time PCR assay with high specificity and accuracy was developed to simultaneously identify Camp. jejuni and detect the gene mutations associated with macrolide resistance.

SIGNIFICANCE AND IMPACT OF THE STUDY

This multiplex method can potentially simplify the identification of Camp. jejuni and determine macrolide resistance due to mutations in 23S rDNA or ribosomal protein L4. This method has a potential for application in different research areas and molecular surveillance.

Effect of estrogen deficiency on the fixation of titanium implants in chronic kidney disease mice

We established a chronic kidney disease (CKD) mouse model with estrogen deficiency and inserted titanium implants into the femur of such mice to investigate the fixation of the implants. Both the histomorphometry and implant resistance indicated that estrogen deficiency impaired the fixation of titanium implants inserted into such mice.

INTRODUCTION

CKD has been regarded as a worldwide public health problem. Estrogen is a critical factor for both renal protection and bone remodeling. A previous study demonstrated that CKD impairs the early healing of titanium implants. However, the combined effect of estrogen deficiency and CKD on the fixation of titanium implants is largely unknown.

METHODS

Forty 9-week-old female C57BL mice were randomly divided into sham, ovariectomy (OVX), CKD, and CKD + OVX groups. Uremia and estrogen deficiency were induced by 5/6 nephrectomy and OVX, respectively. Experimental titanium implants were inserted into the distal end of the femur. Bone-implant contact (BIC) ratio and bone volume (BV/TV) around the implants were histomorphometrically analyzed. The fixation strength of the implant was measured by a biomechanical push-in resistance test.

RESULTS

Serum measurement confirmed a significant increase in serum blood urea nitrogen (BUN) in the CKD group, which was further increased by OVX. Estrogen deficiency led to significant decreases in the BIC ratio, BV/TV, and the push-in resistance in CKD animals. There was a significant interaction between the effects of OVX and CKD, with OVX exacerbating the effects of CKD on BIC ratio and push-in resistance.

CONCLUSIONS

The results indicated that estrogen deficiency exerts a synergistic effect with CKD and further impairs the fixation of titanium implants in CKD mice.

Low-power-threshold photonic saturable absorber in nonlinear chalcogenide glass

We experimentally demonstrate controllable nonlinear modulation of optical guiding in ultrafast laser-written evanescently coupled waveguide arrays in bulk gallium lanthanum sulfide chalcogenide glass. The intensity-dependent response is validated by simulating light propagation in waveguide arrays with instantaneous Kerr nonlinearity using a discrete-continuous spatiotemporal unidirectional Maxwell equation model. The intensity-driven modulation of transmission in multicore structures acts as a potential saturable absorber at kilowatt threshold levels.

Genetic diversity of Y-short tandem repeats in Chinese native cattle breeds

The aim of this study is to use Y-chromosome gene polymorphism method to investigate regional differences in genetic variation and population evolution history of the Chinese native cattle breeds. Six Y-chromosome short tandem repeat (Y-STR) loci (UMN0929, UMN0108, UMN0920, INRA124, UMN2404, and UMN0103) were analyzed using 1016 healthy and heterogenetic males and 90 females of 9 native cattle breeds (Qinchuan, Jinnan, Zaosheng, Luxi, Nanyang, Jiaxian, Dabieshan, Yanbian, and Menggu) in China. Allele frequency and gene diversity were calculated for the various populations. The results indicated that Y-STRs in the 6 loci have polymorphisms and genetic diversity in Chinese cattle populations. The genetic diversity analysis revealed that the Chinese cattle populations have a close genetic relationship. The analysis of INRA124, UMN2404, and UMN0103 loci revealed the original history of Chinese cattle because of which cattle belonging to Bos taurus or Bos indicus could be determined. Interestingly, a declining zebu introgression was displayed from South to North and from East to West in the Chinese geographical distribution, which implied that cattle population from various regions of China had been subjected to somewhat different evolutionary history. This conclusion supported other evidences such as earlier archaeological, historical research, and blood protein polymorphism analysis.

Expression analysis of Gli1 and Gli2 in different tissues and muscle-derived cells of Qinchuan cattle

The Hedgehog (Hh) signaling pathway regulates the differentiation of many kinds of cells and plays a critical role in many embryonic and postnatal developmental processes. Gli1 and Gli2 are two transcription factors of the Hh signaling pathway. In this study, we used quantitative real-time polymerase chain reaction to detect the relative expression of Gli1 and Gli2 in 13 tissues from three two-year-old purebred Qinchuan cattle, as well as in different cell populations derived from muscle and different stages of myogenic differentiation of myoblasts. The expression levels of Gli1 and Gli2 in muscle were the lowest of the 13 tissues (P < 0.05), and they declined predominantly from preplate (pp)1 to pp6 cells. However, the expression of Gli2 was elevated during myogenic differentiation until the 6th day. We speculated that Hh signaling was negatively activated in myocytes and quiescent myoblasts. The increased expression of Gli1 and Gli2 in the early days of myogenic differentiation suggested that Hh signaling would be activated when the quiescent bovine myoblast was stimulated to initiate myogenic differentiation.

Abstract 544: Recurrent DICER1 hotspot mutations in endometrial cancer and their impact on microRNA biogenesis

Alternation in genes associated with microRNA (miRNA) biogenesis pathway may lead to miRNA dysregulation, and is implicated in a variety of human malignancies. Previously our group identified recurrent somatic “hotspot” mutations (E1705, D1709, D1810, E1813) in a critical miRNA-processing gene, DICER1, in rare sex cord-stromal tumors. During miRNA biogenesis, the two RNase III domains of DICER1 form an intramolecular dimer, which leads to the cleavage of the precursor miRNA (pre-miRNA) hairpin and generate mature 5p and 3p miRNAs from 5’ and 3’ arms of the precursor hairpin respectively. Studies have shown that the hotspot mutations in the RNase IIIb metal binding domain could impair DICER1's ability to generate mature 5p miRNAs, leading to global loss of 5p miRNAs.

Recently, in collaboration with The Cancer Genome Atlas (TCGA), we identified DICER1 hotspot mutations in a small subset of endometrial cancer from TCGA cohort (6/248) as well as our own tumor bank (6/307), suggesting disruption of DICER1 is implicated in a common malignancy. We also found an additional recurrent mutation G1809R and demonstrated that it has similar detrimental effects on miRNA biogenesis as hotspot mutations through deep sequencing and realtime PCR. Using Illumina Miseq targeted resequencing and Sanger sequencing, we observed biallelic DICER1 mutations in RNase IIIb domain in some but not all cases. miRNA deep sequencing confirmed that 5p miRNAs are decreased in both cell line models and endometrial tumors with hotspot mutations. Bioinformatic analysis of RNA sequencing profiles from TCGA dataset predicted hotspot DICER1 mutations to have greater functional impact than non-hotspot DICER1 mutations on gene expression. The oncogenic properties of DICER1 hotspot mutations are currently under investigation.

Citation Format: Jiamin Chen, Yemin Wang, Melissa McConechy, Michael Anglesio, Janine Senz, Winnie Yang, Jamie Rosner, Andy Chu, Grace Cheng, Gregg Morin, David Huntsman. Recurrent DICER1 hotspot mutations in endometrial cancer and their impact on microRNA biogenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 544. doi:10.1158/1538-7445.AM2014-544

Multiplexed immunoassay based on micromotors and microscale tags

This work reports on the coupling of antibody-functionalized micromotors and microwire-tagged proteins for rapid and multiplexed immunoassays. While micromotor-induced mixing accelerates the immunoreaction, tagging the proteins with microscopic particles of different sizes and shapes allows for their multiplexed discrimination, alerting of the presence of a biological threat.