Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation

<p>Abstract</p> <p>Background</p> <p>Epstein-Barr virus (EBV) presumably plays an important role in the pathogenesis of nasopharyngeal carcinoma (NPC), but the molecular mechanism of EBV-dependent neoplastic transformation is not well understood. The combination of bioinformatics with evidences from biological experiments paved a new way to gain more insights into the molecular mechanism of cancer.</p> <p>Results</p> <p>We profiled gene expression using a meta-analysis approach. Two sets of meta-genes were obtained. Meta-A genes were identified by finding those commonly activated/deactivated upon EBV infection/reactivation. These genes could be key players for pathways de-regulated by EBV during latent infection and lytic proliferation. Meta-B genes were obtained from differential genes commonly expressed in NPC and PEL (primary effusion lymphoma). We then integrated meta-A, meta-B and associated factors into an interaction network using acquired information. Our analysis suggests that NPC transformation depends on timely regulation of DEK, CDK inhibitor(s), p53, RB and several transcriptional cascades, interconnected by E2F, AP-1, NF-κB, STAT3 among others during latent and lytic cycles.</p> <p>Conclusion</p> <p>In conclusion, our meta-analysis strategy re-analyzed EBV-related tumor data sets and identified sets of meta-genes possibly involved in maintaining latent or switching to lytic cycles of EBV in NPC. The results of this analysis may shed new lights to further our understanding of the EBV-led neoplastic transformation.</p

Suppressed atmospheric chemical aging of cooking organic aerosol particles in wintertime conditions

Cooking organic aerosol (COA) is one of the major constituents of particulate matter in urban areas. COA is oxidized by atmospheric oxidants such as ozone, changing its physical, chemical and toxicological properties. However, atmospheric chemical lifetimes of COA and its tracers such as oleic acid are typically longer than those that have been estimated by laboratory studies. We tackled the issue by considering temperature. Namely, we hypothesize that increased viscosity of COA at ambient temperature accounts for its prolonged atmospheric chemical lifetimes in wintertime. Laboratory-generated COA particles from cooking oil were exposed to ozone in an aerosol flow tube reactor for the temperature range of −20 to 35 °C. The pseudo-second-order chemical reaction rate constants (k2) were estimated from the experimental data by assuming a constant ozone concentration in the flow tube. The estimated values of k2 decreased by orders of magnitude for lower temperatures. The temperature dependence in k2 was fit well by considering the diffusion-limited chemical reaction mechanism. The result suggested that increased viscosity was likely the key factor to account for the decrease in chemical reactivity at the reduced temperature range, though the idea will still need to be verified by temperature-dependent viscosity data in the future. In combination with the observed global surface temperature, the atmospheric chemical lifetimes of COA were estimated to be much longer in wintertime (&gt; 1 h) than in summertime (a few minutes) for temperate and boreal regions. Our present study demonstrates that the oxidation lifetimes of COA particles will need to be parameterized as a function of temperature in the future for estimating environmental impacts and fates of this category of particulate matter.</p

The effect of capsaicin on expression patterns of CGRP in trigeminal ganglion and trigeminal nucleus caudalis following experimental tooth movement in rats

Objectives The aim of this study was to explore the effect of capsaicin on expression patterns of calcitonin gene-related peptide (CGRP) in the trigeminal ganglion (TG) and trigeminal subnucleus caudalis (Vc) following experimental tooth movement. Material and Methods Male Sprague-Dawley rats were used in this study and divided into small-dose capsaicin+force group, large-dose capsaicin+force group, saline+force group, and no force group. Closed coil springs were used to mimic orthodontic forces in all groups except for the no force group, in which springs were inactivated. Capsaicin and saline were injected into periodontal tissues. Rats were euthanized at 0 h, 12 h, 1 d, 3 d, 5 d, and 7 d following experimental tooth movement. Then, TG and Vc were obtained for immunohistochemical staining and western blotting against CGRP. Results Immunohistochemical results indicated that CGRP positive neurons were located in the TG, and CGRP immunoreactive fibers were distributed in the Vc. Immunohistochemical semiquantitative analysis and western blotting analysis demonstrated that CGRP expression levels both in TG and Vc were elevated at 12 h, 1 d, 3 d, 5 d, and 7 d in the saline + force group. However, both small-dose and large-dose capsaicin could decrease CGRP expression in TG and Vc at 1 d and 3 d following experimental tooth movement, as compared with the saline + force group. Conclusions These results suggest that capsaicin could regulate CGRP expression in TG and Vc following experimental tooth movement in rats

Association between cognitive impairment and risk of atrial fibrillation: The Atherosclerosis Risk in Communities study

Background: Atrial fibrillation (AF) is reportedly a risk factor for cognitive impairment. Interestingly, recent studies have emphasized that impaired cognition is probably an initiating factor of cardiovascular disease. Thus, we aimed to explore the association between impaired cognition and the risk of AF, and clarify the potential mechanisms. Methods: Participants of visit 2 (1991–1993) in the Atherosclerosis Risk in Communities study were included. Global cognition z-scores and factor scores were calculated using the word fluency, delayed word recall, and digit symbol substitution tests. AF incidents were diagnosed by electrocardiography and inpatient records. The association of cognitive decline with AF risk and left atrial volume index (LAVI) was explored using Cox proportional hazards and linear regression models, respectively. Results: During the median follow-up of 18.2 ± 6.2 years, 2056/11,675 (17.6%) participants developed AF. Participants in the lowest quartile of global cognition z- and factor scores had a higher risk of AF (hazard ratio [HR]: 1.271, 95% confidence interval [CI]: 1.094–1.477, p = 0.002; HR: 1.305, 95% CI: 1.110–1.535, p = 0.001, respectively) than those in the highest quartile. Global cognition z- and factor scores were negatively correlated with the LAVI (B: –0.411, 95% CI: –0.749 to –0.074, p = 0.017; B: –0.425, 95% CI: –0.833 to –0.017, p = 0.041, respectively). Conclusions: Cognitive decline is significantly associated with a higher risk of AF, with atrial remodeling being a potential mechanism. Our results extend previous findings of the brain-heart axis and indicate the effects of cognitive injury on cardiac function and structure. Registration: URL: https://www.clinicaltrials.gov; unique identifier: NCT0000513

A Study of the Crystallization, Melting, and Foaming Behaviors of Polylactic Acid in Compressed CO2

The crystallization and melting behaviors of linear polylactic acid (PLA) treated by compressed CO2 was investigated. The isothermal crystallization test indicated that while PLA exhibited very low crystallization kinetics under atmospheric pressure, CO2 exposure significantly increased PLA’s crystallization rate; a high crystallinity of 16.5% was achieved after CO2 treatment for only 1 min at 100 °C and 6.89 MPa. One melting peak could be found in the DSC curve, and this exhibited a slight dependency on treatment times, temperatures, and pressures. PLA samples tended to foam during the gas release process, and a foaming window as a function of time and temperature was established. Based on the foaming window, crystallinity, and cell morphology, it was found that foaming clearly reduced the needed time for PLA’s crystallization equilibrium

Interest-driven creator theory: towards a theory of learning design for Asia in the twenty-first century

Asian education is known for its examination-driven orientation, with the downsides of distorting the processes of learning and teaching, diminishing students’ interest in learning, and failing to nurture twenty-first century competencies among students. As a group of Asian researchers, we have been developing Interest-Driven Creator (IDC) Theory, a design theory based on three anchored concepts, namely interest, creation, and habit. Each of these anchored concepts is represented by a loop composed of three components. In the interest loop, the three components are triggering, immersing, and extending. The components of the creation loop are imitating, combining, and staging. The habit loop consists of cuing environment, routine, and harmony. These three loops are interconnected in various ways, with their characteristics revealed by the design process. We hypothesize that technology-supported learning activities that are designed with reference to IDC Theory will enable students to develop interest in learning, be immersed in the creation process, and, by repeating this process in their daily routines, strengthen habits of creation. Furthermore, students will excel in learning performance, develop twenty-first century competencies, and become lifelong interest-driven creators. To sharpen our understanding and further the development of the theory, we need more discussion and collaborative efforts in the community. Hypotheses arising from this theory can be tested, revised, or refined by setting up and investigating IDC Theory-based experimental sites. By disseminating the framework, foundations, and practices to the various countries and regions of Asia, we hope that it will bring about compelling examples and hence a form of quality education for the twenty-first century, which is an alternative to the examination-driven education system. In this paper, we present an overall introduction to IDC Theory and its history, and discuss some of the steps for advancing it in the future

Applications of Aptasensors in Clinical Diagnostics

Aptamers are artificial oligonucleotides (DNA or RNA) selected in vitro that bind a broad range of targets with high affinity and specificity; a sensitive yet simple method to utilize aptamers as recognition elements for the development of biosensors (aptasensors) is to transduce the signal electrochemically. So far, aptasensors have been applied to clinical diagnostics and several technologies are in development. Aptasensors will extend the limits of current clinical diagnostics. Although the potential diagnostic applications are unlimited, the most current applications are foreseen in the areas of biomarker detection, cancer clinical testing, detection of infectious microorganisms and viruses. This review attempts to list examples of the research progresses of aptamers in biosensor platforms that have been published in recent years; in particular, we display cases of aptasensors that are already incorporated in clinical diagnostics or have potential applications in clinical diagnostics

IDC theory: habit and the habit loop

Interest-driven creator (IDC) theory is a design theory that intends to inform the design of future education in Asia. It consists of three anchored concepts, namely, interest, creation, and habit. This paper presents the third anchored concept habit as well as the habit loop. IDC theory assumes that learners, when driven by interest, can be engaged in knowledge creation. Furthermore, by repeating such process in their daily learning routines, learners will form interest-driven creation habits. The habit loop, the process of building such a habit, consists of three component concepts— cuing environment, routine, and harmony. The cuing environment is a habit trigger that tells the students’ brain to get prepared and go into an automatic mode, letting learning behavior unfold. Routine refers to the behavioral patterns the students repeat most often, literally etched into their neural pathways. Harmony refers to the affective outcome of the routine activity as well as the integration or stabilization of habits; that is, through the routine behavior and action, students may feel that their needs get fulfilled, feel satisfied, and experience inner peace. It is our hope that such habitual behavior of creating knowledge can be sustained so long that students ultimately become lifelong interest-driven creators. This paper focuses on the description of the three components of the habit loop and discusses how these components are related to the interest loop and the creation loop in supporting learners in developing their interest-driven creation capability

Whole-genome sequencing of <em>Oryza brachyantha</em> reveals mechanisms underlying <em>Oryza</em> genome evolution

The wild species of the genus Oryza contain a largely untapped reservoir of agronomically important genes for rice improvement. Here we report the 261-Mb de novo assembled genome sequence of Oryza brachyantha. Low activity of long-terminal repeat retrotransposons and massive internal deletions of ancient long-terminal repeat elements lead to the compact genome of Oryza brachyantha. We model 32,038 protein-coding genes in the Oryza brachyantha genome, of which only 70% are located in collinear positions in comparison with the rice genome. Analysing breakpoints of non-collinear genes suggests that double-strand break repair through non-homologous end joining has an important role in gene movement and erosion of collinearity in the Oryza genomes. Transition of euchromatin to heterochromatin in the rice genome is accompanied by segmental and tandem duplications, further expanded by transposable element insertions. The high-quality reference genome sequence of Oryza brachyantha provides an important resource for functional and evolutionary studies in the genus Oryza

Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae

Engineering Saccharomyces cerevisiae for biodegradation and transformation of industrial toxic substances such as catechol (CA) has received widespread attention, but the low tolerance of S. cerevisiae to CA has limited its development. The exploration and modification of genes or pathways related to CA tolerance in S. cerevisiae is an effective way to further improve the utilization efficiency of CA. This study identified 36 genes associated with CA tolerance in S. cerevisiae through genome-wide identification and bioinformatics analysis and the ERG6 knockout strain (ERG6Δ) is the most sensitive to CA. Based on the omics analysis of ERG6Δ under CA stress, it was found that ERG6 knockout affects pathways such as intrinsic component of membrane and pentose phosphate pathway. In addition, the study revealed that 29 genes related to the cell wall-membrane system were up-regulated by more than twice, NADPH and NADP+ were increased by 2.48 and 4.41 times respectively, and spermidine and spermine were increased by 2.85 and 2.14 times, respectively, in ERG6Δ. Overall, the response of cell wall-membrane system, the accumulation of spermidine and NADPH, as well as the increased levels of metabolites in pentose phosphate pathway are important findings in improving the CA resistance. This study provides a theoretical basis for improving the tolerance of strains to CA and reducing the damage caused by CA to the ecological environment and human health