Gene expression profiling of oxidative stress response of C. elegans aging defective AMPK mutants using massively parallel transcriptome sequencing

<p>Abstract</p> <p>Background</p> <p>A strong association between stress resistance and longevity in multicellular organisms has been established as many mutations that extend lifespan also show increased resistance to stress. AAK-2, the <it>C. elegans </it>homolog of an alpha subunit of AMP-activated protein kinase (AMPK) is an intracellular fuel sensor that regulates cellular energy homeostasis and functions in stress resistance and lifespan extension.</p> <p>Findings</p> <p>Here, we investigated global transcriptional responses of <it>aak-2 </it>mutants to oxidative stress and in turn identified potential downstream targets of AAK-2 involved in stress resistance in <it>C. elegans</it>. We employed massively parallel Illumina sequencing technology and performed comprehensive comparative transcriptome analysis. Specifically, we compared the transcriptomes of <it>aak-2 </it>and wild type animals under normal conditions and conditions of induced oxidative stress. This research has presented a snapshot of genome-wide transcriptional activities that take place in <it>C. elegans </it>in response to oxidative stress both in the presence and absence of AAK-2.</p> <p>Conclusions</p> <p>The analysis presented in this study has enabled us to identify potential genes involved in stress resistance that may be either directly or indirectly under the control of AAK-2. Furthermore, we have extended our current knowledge of general defense responses of <it>C. elegans </it>against oxidative stress supporting the function for AAK-2 in inhibition of biosynthetic processes, especially lipid synthesis, under oxidative stress and transcriptional regulation of genes involved in reproductive processes.</p

Evaluation of a genomic classifier in radical prostatectomy patients with lymph node metastasis.

OBJECTIVE: To evaluate the performance of the Decipher test in predicting lymph node invasion (LNI) on radical prostatectomy (RP) specimens. METHODS: We identified 1,987 consecutive patients with RP who received the Decipher test between February and August 2015 (contemporary cohort). In the contemporary cohort, only the Decipher score from RP specimens was available for analysis. In addition, we identified a consecutive cohort of patients treated with RP between 2006 and 2012 at the University of California, San Diego, with LNI upon pathologic examination (retrospective cohort). The retrospective cohort yielded seven, 22, and 18 tissue specimens from prostate biopsy, RP, and lymph nodes (LNs) for individual patients, respectively. Univariable and multivariable logistic regression analyses were used to evaluate the performance of Decipher in the contemporary cohort with LNI as the endpoint. In the retrospective cohort, concordance of risk groups was assessed using validated cut-points for low (0.60) Decipher scores. RESULTS: In the contemporary cohort, 51 (2.6%) patients had LNI. Decipher had an odds ratio of 1.73 (95% confidence interval, 1.46-2.05) and 1.42 (95% confidence interval, 1.19-1.7) per 10% increase in score on univariable and multivariable (adjusting for pathologic Gleason score, extraprostatic extension, and seminal vesicle invasion), respectively. No significant difference in the clinical and pathologic characteristics between the LN positive patients of contemporary and retrospective cohorts was observed (all P\u3e0.05). Accordingly, among LN-positive patients in the contemporary cohort and retrospective cohort, 80% and 77% had Decipher high risk scores (P=1). In the retrospective cohort, prostate biopsy cores with the highest Gleason grade and percentage of tumor involvement had 86% Decipher risk concordance with both RP and LN specimens. CONCLUSION: Decipher scores were highly concordant between pre- and post-surgical specimens. Further, Decipher scores from RP tissue were predictive of LNI at RP. If validated in a larger cohort of prostate biopsy specimens for prediction of adverse pathology at RP, Decipher may be useful for improved pre-operative staging

Associations of reproductive factors with incidence of myocardial infarction and ischemic stroke in postmenopausal women: a cohort study

Background To assess the association between the reproductive factors of age at menarche, age at menopause, and reproductive span and the incidence of myocardial infarction (MI) and ischemic stroke (IS). Methods We used a population-based retrospective cohort study from the National Health Insurance Service database of Korea including a total of 1,224,547 postmenopausal women. Associations between age at menarche (≤ 12, 13–14 [reference], 15, 16, and ≥ 17years), age at menopause (< 40, 40–45, 46–50, 51–54 [reference], and ≥ 55years), and reproductive span (< 30, 30–33, 34–36, 37–40 [reference], and ≥ 41years) and the incidence of MI and IS were assessed by Cox proportional hazard models with adjustment for traditional cardiovascular risk factors and various reproductive factors. Results During a median follow-up of 8.4years, 25,181 MI and 38,996 IS cases were identified. Late menarche (≥ 16years), early menopause (≤ 50years), and short reproductive span (≤ 36years) were linearly associated with a 6%, 12–40%, and 12–32% higher risk of MI, respectively. Meanwhile, a U-shaped association between age at menarche and risk of IS was found, with a 16% higher risk in early menarche (≤ 12years) and a 7–9% higher risk in late menarche (≥ 16years). Short reproductive span was linearly associated with an increased risk of MI, whereas both shorter and longer reproductive spans were associated with an increased risk of IS. Conclusions This study demonstrated different patterns of association between age at menarche and incidence of MI and IS: a linear association for MI versus a U-shaped association for IS. Female reproductive factors in addition to traditional cardiovascular risk factors should be considered when assessing overall cardiovascular risk in postmenopausal women

Evaluation of a genomic classifier in radical prostatectomy patients with lymph node metastasis

OBJECTIVE: To evaluate the performance of the Decipher test in predicting lymph node invasion (LNI) on radical prostatectomy (RP) specimens. METHODS: We identified 1,987 consecutive patients with RP who received the Decipher test between February and August 2015 (contemporary cohort). In the contemporary cohort, only the Decipher score from RP specimens was available for analysis. In addition, we identified a consecutive cohort of patients treated with RP between 2006 and 2012 at the University of California, San Diego, with LNI upon pathologic examination (retrospective cohort). The retrospective cohort yielded seven, 22, and 18 tissue specimens from prostate biopsy, RP, and lymph nodes (LNs) for individual patients, respectively. Univariable and multivariable logistic regression analyses were used to evaluate the performance of Decipher in the contemporary cohort with LNI as the endpoint. In the retrospective cohort, concordance of risk groups was assessed using validated cut-points for low (<0.45), intermediate (0.45–0.60), and high (>0.60) Decipher scores. RESULTS: In the contemporary cohort, 51 (2.6%) patients had LNI. Decipher had an odds ratio of 1.73 (95% confidence interval, 1.46–2.05) and 1.42 (95% confidence interval, 1.19–1.7) per 10% increase in score on univariable and multivariable (adjusting for pathologic Gleason score, extraprostatic extension, and seminal vesicle invasion), respectively. No significant difference in the clinical and pathologic characteristics between the LN positive patients of contemporary and retrospective cohorts was observed (all P>0.05). Accordingly, among LN-positive patients in the contemporary cohort and retrospective cohort, 80% and 77% had Decipher high risk scores (P=1). In the retrospective cohort, prostate biopsy cores with the highest Gleason grade and percentage of tumor involvement had 86% Decipher risk concordance with both RP and LN specimens. CONCLUSION: Decipher scores were highly concordant between pre- and post-surgical specimens. Further, Decipher scores from RP tissue were predictive of LNI at RP. If validated in a larger cohort of prostate biopsy specimens for prediction of adverse pathology at RP, Decipher may be useful for improved pre-operative staging

The multiplex bead array approach to identifying serum biomarkers associated with breast cancer

Introduction Breast cancer is the most common type of cancer seen in women in western countries. Thus, diagnostic modalities sensitive to early-stage breast cancer are needed. Antibody-based array platforms of a data-driven type, which are expected to facilitate more rapid and sensitive detection of novel biomarkers, have emerged as a direct, rapid means for profiling cancer-specific signatures using small samples. In line with this concept, our group constructed an antibody bead array panel for 35 analytes that were selected during the discovery step. This study was aimed at testing the performance of this 35-plex array panel in profiling signatures specific for primary non-metastatic breast cancer and validating its diagnostic utility in this independent population. Methods Thirty-five analytes were selected from more than 50 markers through screening steps using a serum bank consisting of 4,500 samples from various types of cancer. An antibody-bead array of 35 markers was constructed using the Luminex (TM) bead array platform. A study population consisting of 98 breast cancer patients and 96 normal subjects was analysed using this panel. Multivariate classification algorithms were used to find discriminating biomarkers and validated with another independent population of 90 breast cancer and 79 healthy controls. Results Serum concentrations of epidermal growth factor, soluble CD40-ligand and proapolipoprotein A1 were increased in breast cancer patients. High-molecular-weight-kininogen, apolipoprotein A1, soluble vascular cell adhesion molecule-1, plasminogen activator inhibitor-1, vitamin-D binding protein and vitronectin were decreased in the cancer group. Multivariate classification algorithms distinguished breast cancer patients from the normal population with high accuracy (91.8% with random forest, 91.5% with support vector machine, 87.6% with linear discriminant analysis). Combinatorial markers also detected breast cancer at an early stage with greater sensitivity. Conclusions The current study demonstrated the usefulness of the antibody-bead array approach in finding signatures specific for primary non-metastatic breast cancer and illustrated the potential for early, high sensitivity detection of breast cancer. 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A Pedagogical Study of the Four Lauds for Solo Violin by Elliott Carter

Elliott Carter was one of the most influential composers of the past century, leaving a diverse and prolific body of over 150 works to posterity. Along with the Violin Concerto and “Mnemosyné,” the Four Lauds are the only works written for solo violin. Literature on these pieces is not extensive thus far, and this dissertation will provide an introduction to any student who is interested in learning about Carter’s violin music. In the first chapter, I will discuss relevant aspects of Carter’s musical language such as his use of all-trichord hexachord, all-interval trichord, complement union property, and his ideas on time. Then I will study each Laud in the following four chapters using a dialogue form between teacher and student, bringing together elements of performance, theory, and pedagogy

Application of next-generation sequencing for comparative transcriptome analysis

I have used novel whole transcriptome sequence data generated from massively parallel high-throughput next generation sequencing technologies, namely 454 pyrosequencing and Illumina sequencing, to perform comparative transcriptome analyses of C. elegans populations in specific biological conditions and developmental stages. Firstly, I have conducted transcriptome profiling of C. elegans in its first larval (L1) stage using data generated from the Roche 454 sequencing platform. I have used this data to refine gene structures, identify putative novel transcripts, and characterize the L1 specific transcriptome. Secondly, I have taken Illumina paired-end sequencing transcriptome data generated from starved and fed populations of C. elegans in the L1 stage and investigated metabolic and developmental gene expression changes that are specific to this developmental stage. Additionally I have taken advantage of this paired-end data to perform de novo assembly of the short tag sequences to identify novel transcript structures with confirmed splice sites, providing greater confidence in novel gene structure discovery. Lastly, I have investigated global transcriptional responses to oxidative stress in aging defective aak-2 mutants. This analysis has led to the identification of potential downstream targets of the AMP-activated protein kinase, AAK-2, which is known to be involved in stress resistance and lifespan control in C. elegans. This study demonstrates the impact of new high-throughput sequencing technologies on genomic analysis, providing valuable insight into transcriptome complexity as a result of developmental, metabolic, and mutational effects in C. elegans. The approaches I have described here can be applied to transcriptome analyses of more complex organisms ultimately leading to investigation of transcriptional changes in human diseases

Effect of Loading and Beam Sizes on the Structural Behaviors of Reinforced Concrete Beams Under and After Fire

Abstract Performance-based fire resistance design needs consideration of various influencing parameters of structures such as load levels and cross-sectional size. Therefore, the studies of fire damaged reinforced concrete (RC) structures are performed experimentally and analytically. Twelve RC beams with different load levels and cross sections are exposed to high temperatures following the ISO 834 standard time temperature. After the fire test, the fire-damaged beams are loaded using four-point loading to obtain its residual strength. In addition, ABAQUS 6.10-3 is used to preform structural analyses of the ductility of the fire-damaged beams. The results indicate that the temperature, stiffness and ductility of the fire-damaged beams are significantly influenced by the load level, cross-sectional size and time exposed to fire. Also, the ductility of the fire-damaged beam can be predicted using an analytical method, which is not easy to otherwise determine experimentally