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Find video protocols related to scientific articles indexed in Pubmed.
Identification of chimeric TSNAX-DISC1 resulting from intergenic splicing in endometrial carcinoma through high-throughput RNA sequencing.
Carcinogenesis
PUBLISHED: 09-19-2014
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Gene fusion is among the primary processes that generate new genes and has been well characterized as potent pathway of oncogenesis. Here, by high-throughput RNA sequencing in nine paired human endometrial carcinoma (EC) and matched non-cancerous tissues, we obtained that chimeric translin-associated factor X-disrupted-in-schizophrenia 1 (TSNAX-DISC1) occurred significantly upregulated in multiple EC samples. Experimental investigation showed that TSNAX-DISC1 appears to be formed by splicing without chromosomal rearrangement. The chimera expression inversely correlated with the binding of CCCTC-binding factor (CTCF) to the insulators. Subsequent investigations indicate that long intergenic non-coding RNA lincRNA-NR_034037, separating TSNAX from DISC1, regulates TSNAX -DISC1 production and TSNAX/DISC1 expression levels by extricating CTCF from insulators. Dysregulation of TSNAX influences steroidogenic factor-1-stimulated transcription on the StAR promoter, altering progesterone actions, implying the association with cancer. Together, these results advance our understanding of the mechanism in which lincRNA-NR_034037 regulates TSNAX-DISC1 formation programs that tightly regulate EC development.
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Form-cue invariant second-order neuronal responses to contrast modulation in primate area V2.
J. Neurosci.
PUBLISHED: 09-05-2014
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A fundamental task of the visual system is to extract figure-ground boundaries between images of objects, which in natural scenes are often defined not only by luminance differences but also by "second-order" contrast or texture differences. Responses to contrast modulation (CM) and other second-order stimuli have been extensively studied in human psychophysics, but the neuronal substrates of second-order responses in nonhuman primates remain poorly understood. In this study, we have recorded single neurons in area V2 of macaque monkeys, using both CM patterns as well as conventional luminance modulation (LM) gratings. CM stimuli were constructed from stationary sine wave grating carrier patterns, which were modulated by drifting envelope gratings of a lower spatial frequency. We found approximately one-third of visually responsive V2 neurons responded to CM stimuli with a pronounced selectivity to carrier spatial frequencies, and often orientations, that were clearly outside the neurons' passbands for LM gratings. These neurons were "form-cue invariant" in that their tuning to CM envelope spatial frequency and orientation was very similar to that for LM gratings. Neurons were tuned to carrier spatial frequencies that were typically 2-4 octaves higher than their optimal envelope spatial frequencies, similar to results from human psychophysics. These results are distinct from CM responses arising from surround suppression, but could be understood in terms of a filter-rectify-filter model. Such neurons could provide a functionally useful and explicit representation of segmentation boundaries as well as a plausible neural substrate for human perception of second-order boundaries.
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Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations.
Chen Wu, Zhaoming Wang, Xin Song, Xiao-Shan Feng, Christian C Abnet, Jie He, Nan Hu, Xian-Bo Zuo, Wen Tan, Qimin Zhan, Zhibin Hu, Zhonghu He, Weihua Jia, Yifeng Zhou, Kai Yu, Xiao-Ou Shu, Jian-Min Yuan, Wei Zheng, Xue-Ke Zhao, She-Gan Gao, Zhi-Qing Yuan, Fu-You Zhou, Zong-Min Fan, Ji-Li Cui, Hong-Li Lin, Xue-Na Han, Bei Li, Xi Chen, Sanford M Dawsey, Linda Liao, Maxwell P Lee, Ti Ding, You-Lin Qiao, Zhihua Liu, Yu Liu, Dianke Yu, Jiang Chang, Lixuan Wei, Yu-Tang Gao, Woon-Puay Koh, Yong-Bing Xiang, Ze-Zhong Tang, Jin-Hu Fan, Jing-jing Han, Sheng-Li Zhou, Peng Zhang, Dong-Yun Zhang, Yuan Yuan, Ying Huang, Chunling Liu, Kan Zhai, Yan Qiao, Guangfu Jin, Chuanhai Guo, Jianhua Fu, Xiaoping Miao, Changdong Lu, Haijun Yang, Chaoyu Wang, William A Wheeler, Mitchell Gail, Meredith Yeager, Jeff Yuenger, Er-Tao Guo, Ai-li Li, Wei Zhang, Xue-Min Li, Liang-Dan Sun, Bao-Gen Ma, Yan Li, Sa Tang, Xiu-Qing Peng, Jing Liu, Amy Hutchinson, Kevin Jacobs, Carol Giffen, Laurie Burdette, Joseph F Fraumeni, Hongbing Shen, Yang Ke, Yixin Zeng, Tangchun Wu, Peter Kraft, Charles C Chung, Margaret A Tucker, Zhi-Chao Hou, Ya-Li Liu, Yan-Long Hu, Li Wang, Guo Yuan, Li-Sha Chen, Xiao Liu, Teng Ma, Hui Meng, Li Sun, Xin-Min Li, Xiu-Min Li, Jian-Wei Ku, Ying-Fa Zhou, Liu-Qin Yang, Zhou Wang, Yin Li, Qirenwang Qige, Wen-jun Yang, Guang-Yan Lei, Long-qi Chen, En-Min Li, Ling Yuan, Wen-Bin Yue, Ran Wang, Lu-Wen Wang, Xue-Ping Fan, Fang-Heng Zhu, Wei-Xing Zhao, Yi-min Mao, Mei Zhang, Guo-Lan Xing, Ji-Lin Li, Min Han, Jing-Li Ren, Bin Liu, Shu-Wei Ren, Qing-Peng Kong, Feng Li, Ilyar Sheyhidin, Wu Wei, Yan-Rui Zhang, Chang-Wei Feng, Jin Wang, Yu-Hua Yang, Hong-Zhang Hao, Qi-De Bao, Bao-Chi Liu, Ai-Qun Wu, Dong Xie, Wan-Cai Yang, Liang Wang, Xiao-Hang Zhao, Shu-Qing Chen, Jun-Yan Hong, Xue-Jun Zhang, Neal D Freedman, Alisa M Goldstein, Dongxin Lin, Philip R Taylor, Li-dong Wang, Stephen J Chanock.
Nat. Genet.
PUBLISHED: 08-17-2014
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We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) of esophageal squamous cell carcinoma (ESCC) in individuals of Chinese ancestry (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% confidence interval (CI) = 0.82-0.88; P = 7.72 × 10(-20)) and rs1642764 at 17p13.1 (per-allele OR = 0.88, 95% CI = 0.85-0.91; P = 3.10 × 10(-13)). rs7447927 is a synonymous SNP in TMEM173, and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR = 1.33, 95% CI = 1.22-1.46; P = 1.99 × 10(-10)). Our joint analysis identifies new ESCC susceptibility loci overall as well as a new locus unique to the population in the Taihang Mountain region at high risk of ESCC.
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A normative framework for the study of second-order sensitivity in vision.
J Vis
PUBLISHED: 08-07-2014
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While the contrast sensitivity approach has been successful in evaluating the processing of first-order stimuli, there is a need to develop comparable ways of assessing second-order vision. Our purpose here is to establish normative data on second-order contrast-, orientation-, and motion-modulation sensitivity in humans. We propose a unified framework, applying the quick contrast sensitivity function (qCSF) method, which was recently developed for the rapid measurement of contrast sensitivity across the full spatial-frequency range (Lesmes, Lu, Baek, & Albright, 2010), to measure both first- and second-order sensitivity functions. We first show that the qCSF methodology can be successfully adapted to different kinds of first- and second-order measurements. We provide a normative dataset for both first- and second-order sensitivity, and we show that the sensitivity to all these stimuli is equal in the two eyes. Our results confirm some strong differences between first- and second-order processing, in accordance with the classical filter-rectify-filter model. They suggest a common contrast detection mechanism but different second-order mechanisms.
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Manipulation of orbital angular momentum beams based on space diffraction compensation.
Opt Express
PUBLISHED: 08-05-2014
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We put forward a technique to manipulate the size of orbital angular momentum (OAM) beams based on space diffraction compensation. Paraxial Fresnel diffraction which carries a negative spatial quadratic phase distribution can be regarded as a negative diffractive effect. To compensate the negative diffraction, we employ a 4f Fourier lens system containing a phase mask to generate an inverse quadratic phase. The size of OAM beams can be easily controlled by designing the phase mask profile without changing the OAM. The applications of space diffraction compensation in OAM demultiplexing, ring fiber coupling for OAM beams and optical manipulation of micro particles are also discussed.
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Genetic variant in the 3'-untranslated region of VEGFR1 gene influences chronic obstructive pulmonary disease and lung cancer development in Chinese population.
Mutagenesis
PUBLISHED: 06-02-2014
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Lung inflammation and epithelial to mesenchymal transition (EMT) are two pathogenic features for the two contextual diseases: chronic obstructive pulmonary disease (COPD) and lung cancer. VEGFR1 (or FLT1) plays a certain role in promoting tumour growth, inflammation and EMT. To simultaneously test the association between the single nucleotide polymorphisms (SNPs) in VEGFR1 and risk of COPD and lung cancer would reveal genetic mechanisms shared by these two diseases and joint aetiology. We conducted a two-population hospital-based case-control study. Three potential functional SNPs (rs664393, rs7326277 and rs9554314) were genotyped in southern Chinese and validated in eastern Chinese to explore their associations with COPD risk in 1511 COPD patients and 1677 normal lung function controls, and with lung cancer risk in 1559 lung cancer cases and 1679 cancer-free controls. We also detected the function of the promising SNP. Individuals carrying the rs7326277C (CT+CC) variant genotypes of VEGFR1 had a significant decrease in risk of both COPD (OR = 0.78; 95% CI = 0.68-0.90) and lung cancer (OR = 0.79; 95% CI = 0.64-0.98), compared with those carrying the rs7326277TT genotype. Functional assays further showed that the rs7326277C genotypes had lower transcriptional activity and caused decreased VEGFR expression, compared with the rs7326277TT genotype. However, no significant association was observed for the other two SNPs (rs664393 and rs9554314) and either COPD or lung cancer risk. Our data suggested that the rs7326277C variant of VEGFR1 could reduce both COPD and lung cancer risk by lowering VEGFR1 mRNA expression; the SNP might be a common susceptible locus for both COPD and lung cancer.
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A functional polymorphism in the 3'-UTR of PXR interacts with smoking to increase lung cancer risk in southern and eastern Chinese smoker.
Int J Mol Sci
PUBLISHED: 05-20-2014
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Pregnane X receptor (PXR) is an important member of the nuclear receptor superfamily that copes with various endobiotic and xenobiotic stimuli, such as carcinogens by regulating an array of environmental response genes. Low PXR expression has been shown to promote tumor initiation and metastasis. The aim of the current study was to investigate whether the single nucleotide polymorphisms (SNPs) of PXR could alter lung cancer susceptibility in Chinese by affecting the function or expression of PXR. We genotyped three putatively functional SNPs of PXR (i.e., rs3814055C>T, rs3732360C>T, and rs3814058C>T) and analyzed their associations with lung cancer risk in a two-stage case-control study with a total of 1559 lung cancer cases and 1679 controls in the southern and eastern Chinese population. We found that in comparison to the rs3814058CC common genotype, the rs3814058T variants (TC/TT) which is located in the 3'-untranslated region (3'-UTR) of PXR conferred a consistently increased risk of lung cancer in both the southern Chinese (odd ratios (OR)=1.24, 95% confidence interval (CI)=1.03-1.49) and the eastern Chinese (OR=1.33, 95% CI=1.02-1.75). The variants also significantly interacted with smoking on increasing cancer risk (p=0.023). Moreover, lung cancer tissues with the rs3814058T variants showed significantly lower PXR expression than those with rs3814058CC genotype in the smokers (p=0.041). These results suggested that the rs3814058C>T polymorphism of PXR interacts with smoking on increasing lung cancer risk in Chinese smokers, which might be a functional genetic biomarker for lung cancer.
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Contrast Sensitivity Function after Correcting Residual Wavefront Aberrations during RGP Lens Wear.
Optom Vis Sci
PUBLISHED: 04-29-2014
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To investigate the effect on the contrast sensitivity function (CSF) of correcting the residual wavefront aberrations in myopic and keratoconic subjects wearing rigid gas permeable (RGP) contact lenses.
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Immature visual neural system in children reflected by contrast sensitivity with adaptive optics correction.
Sci Rep
PUBLISHED: 03-27-2014
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This study aimed to explore the neural development status of the visual system of children (around 8 years old) using contrast sensitivity. We achieved this by eliminating the influence of higher order aberrations (HOAs) with adaptive optics correction. We measured HOAs, modulation transfer functions (MTFs) and contrast sensitivity functions (CSFs) of six children and five adults with both corrected and uncorrected HOAs. We found that when HOAs were corrected, children and adults both showed improvements in MTF and CSF. However, the CSF of children was still lower than the adult level, indicating the difference in contrast sensitivity between groups cannot be explained by differences in optical factors. Further study showed that the difference between the groups also could not be explained by differences in non-visual factors. With these results we concluded that the neural systems underlying vision in children of around 8 years old are still immature in contrast sensitivity.
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Duplicated copy of CHRNA7 increases risk and worsens prognosis of COPD and lung cancer.
Eur. J. Hum. Genet.
PUBLISHED: 03-16-2014
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Recent genome-wide association studies implicated that the nicotinic acetylcholine receptors (nAChRs) are common susceptible genes of two contextual diseases: chronic obstructive pulmonary disease (COPD) and lung cancer. We aimed to test whether the copy number variations (CNVs) in nAChRs have hereditary contributions to development of the two diseases. In two, two-stage, case-control studies of southern and eastern Chinese, a common CNV-3956 that duplicates the cholinergic receptor, nicotinic, ?7 (CHRNA7) gene was genotyped in a total of 7880 subjects and its biological phenotype was assessed. The ?4-copy of CNV-3956 increased COPD risk (?4-copy vs 2/3-copy: OR=1.44, 95% CI=1.23-1.68) and caused poor lung function, and it similarly augmented risk (OR=1.49, 95% CI=1.29-1.73) and worsened prognosis (hazard ratio (HR)=1.25, 95% CI=1.07-1.45) of lung cancer. The ?4-copy was estimated to account for 1.56% of COPD heritability and 1.87% of lung cancer heritability, respectively. Phenotypic analysis further showed that the ?4-copy of CNV-3956 improved CHRNA7 expression in vivo and increased the carriers' smoking amount. The CNV-3956 of CHRNA7 contributed to increased risks and poor prognoses of both COPD and lung cancer, and this may be a genetic biomarker of the two diseases.European Journal of Human Genetics advance online publication, 19 November 2014; doi:10.1038/ejhg.2014.229.
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Increased levels of the long intergenic non-protein coding RNA POU3F3 promote DNA methylation in esophageal squamous cell carcinoma cells.
Gastroenterology
PUBLISHED: 02-25-2014
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Thousands of long intergenic non-protein coding RNAs (lincRNAs) have been identified in mammals via genome-wide sequencing studies. Many are functional, but are expressed aberrantly by cancer cells. We investigated whether levels of lincRNAs are altered during the development of esophageal squamous cell carcinoma (ESCC).
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Changes of spatial and temporal frequency tuning properties of neurons in the middle temporal area of aged rhesus monkeys.
Eur. J. Neurosci.
PUBLISHED: 01-15-2014
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Aged humans exhibit severe deficits in visual motion perception and contrast sensitivity under various levels of spatial and temporal modulation. Previous studies indicated that many of these deficits are probably mediated by the neural degradation of the central visual system. To clarify the neuronal response mechanisms underlying the visual degradation during aging, we examined the spatial and temporal frequency tuning properties of neurons from anesthetised and paralysed aged monkeys at the middle temporal area (area MT), which is downstream of the primary visual cortex in the visual processing pathway and thought to be critical for motion perception. We found that the preferred spatial and temporal frequencies, spatial resolution and high temporal frequency cutoff of area MT neurons were reduced in aged monkeys, and were accompanied by the broadened tuning width of spatial frequency, elevated spontaneous activity, and decreased signal-to-noise ratio. These results showed that, for neurons in area MT, aging significantly changed both the spatial and temporal frequency response tuning properties. Such evidence provides new insight into the changes occurring at the electrophysiological level that may be related to the aging-related visual deficits, especially in processing spatial and temporal information.
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Processing Deficits of Motion of Contrast-Modulated Gratings in Anisometropic Amblyopia.
PLoS ONE
PUBLISHED: 01-01-2014
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Several studies have indicated substantial processing deficits for static second-order stimuli in amblyopia. However, less is known about the perception of second-order moving gratings. To investigate this issue, we measured the contrast sensitivity for second-order (contrast-modulated) moving gratings in seven anisometropic amblyopes and ten normal controls. The measurements were performed with non-equated carriers and a series of equated carriers. For comparison, the sensitivity for first-order motion and static second-order stimuli was also measured. Most of the amblyopic eyes (AEs) showed reduced sensitivity for second-order moving gratings relative to their non-amblyopic eyes (NAEs) and the dominant eyes (CEs) of normal control subjects, even when the detectability of the noise carriers was carefully controlled, suggesting substantial processing deficits of motion of contrast-modulated gratings in anisometropic amblyopia. In contrast, the non-amblyopic eyes of the anisometropic amblyopes were relatively spared. As a group, NAEs showed statistically comparable performance to CEs. We also found that contrast sensitivity for static second-order stimuli was strongly impaired in AEs and part of the NAEs of anisometropic amblyopes, consistent with previous studies. In addition, some amblyopes showed impaired performance in perception of static second-order stimuli but not in that of second-order moving gratings. These results may suggest a dissociation between the processing of static and moving second-order gratings in anisometropic amblyopia.
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A Newfound association between MDC1 functional polymorphism and lung cancer risk in Chinese.
PLoS ONE
PUBLISHED: 01-01-2014
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Mediator of DNA damage checkpoint protein 1 (MDC1) plays an early and core role in Double-Strand Break Repair (DDR) and ataxia telangiectasia-mutated (ATM) mediated response to DNA double-strand breaks (DSBs), and thus involves the pathogenesis of several DNA damage-related diseases such as cancer. We hypothesized that the single nucleotide polymorphisms (SNPs) of MDC1 which have potencies on affecting MDC1 expression or function were associated with risk of lung cancer. In a two-stage case-control study, we tested the association between 5 putatively functional SNPs of MDC1 and lung cancer risk in a southern Chinese population, and validated the promising association in an eastern Chinese population. We found the SNP rs4713354A>C that is located in the 5'-untranslated region of MDC1 was significantly associated with lung cancer risk in both populations (P = 0.024), with an odds ratio as 1.23(95% confidence interval ?= 1.35-1.26) for the rs4713354C (CA+CC) genotypes compared to the rs4713354AA genotype. However, no significant association was observed between other SNPs and lung cancer risk. The gene-based analysis rested with these SNPs suggested the MDC1 as a susceptible gene for lung cancer (P = 0.009). Moreover, by querying the gene expression database, we further found that the rs4713354C genotypes confer a significantly lower mRNA expression of MDC1 than the rs4713354AA genotype in 260 cases of lymphoblastoid cells (P = 0.002). Our data suggested that the SNP rs4713354A>C of MDC1 may be a functional genetic biomarker for susceptibility to lung cancer in Chinese.
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Declined contrast sensitivity of neurons along the visual pathway in aging cats.
Front Aging Neurosci
PUBLISHED: 01-01-2014
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Changes in the visual cortex appear to mediate much of the visual degradation during normal aging. However, how aging affects different stages along the visual pathway is unclear. In the current study, the contrast response function, one of the most important properties of neurons from early visual areas to high brain areas, was systematically compared along the visual pathway, including the lateral geniculate nucleus (LGN), early visual cortices (A17 and A18), and posteromedial lateral suprasylvian cortex (PMLS, analog to the medial temporal area (MT) in monkeys) of young and old cats. We found that the effects of aging on the LGN were negligible, whereas those in the striate cortex were substantial, with even more severe degradation in the PMLS. Reduced contrast sensitivity of neurons in the three cortical areas was accompanied by enhanced maximal visual response, increased spontaneous activity, and decreased signal-to-noise ratio, while LGN neurons exhibited largely normal response properties. Our results suggested that there was a progressively greater effect of aging on neurons at successively higher stages in the visual pathway.
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A polymorphism rs12325489C>T in the lincRNA-ENST00000515084 exon was found to modulate breast cancer risk via GWAS-based association analyses.
PLoS ONE
PUBLISHED: 01-01-2014
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Breast cancer, one of the most common malignancies diagnosed among women worldwide, is a complex polygenic disease in the etiology of which genetic factors play an important role. Thus far, a subset of breast cancer genetic susceptibility loci has been addressed among Asian woman through genome-wide association studies (GWASs). In this study, we identified numerous long, intergenic, noncoding RNAs (lincRNAs) enriched in these breast cancer risk-related loci and identified 16 single nucleotide polymorphisms (SNPs) located within the sequences of lincRNA exonic regions. We examined whether these 16 SNPs are associated with breast cancer risk in 2539 cancer patients and 2818 control subjects from eastern, southern, and northern Chinese populations. We found that the C allele of the rs12325489C>T polymorphism in the exonic regions of lincRNA-ENST00000515084 was associated with a significantly increased risk of breast cancer (adjusted odds ratio [OR]?=?1.79; 95% confidence interval [CI]?=?1.50-2.12), compared with the rs12325489TT genotype. Biochemical analysis demonstrated that the C to T base change at rs12325489C>T disrupts the binding site for miRNA-370, thereby influencing the transcriptional activity of lincRNA-ENST00000515084 in vitro and in vivo, and affecting cell proliferation and tumor growth. Our findings indicate that the rs12325489C>T polymorphism in the lincRNA-ENST00000515084 exon may be a genetic modifier in the development of breast cancer.
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Cerebral activity to opposite-sex voices reflected by event-related potentials.
PLoS ONE
PUBLISHED: 01-01-2014
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Human voice is a gender discriminating cue and is important to mate selection. This study employed electrophysiological recordings to examine whether there is specific cerebral activity when presented with opposite-sex voices as compared to same-sex voices. Male voices and female voices were pseudo-randomly presented to male and female participants. In Experiment 1, participants were instructed to determine the gender of each voice. A late positivity (LP) response around 750 ms after voice onset was elicited by opposite-sex voices, as reflected by a positive deflection of the ERP to opposite-sex voices than that to same-sex voices. This LP response was prominent around parieto-occipital recording sites, and it suggests an opposite-sex specific process, which may reflect emotion- and/or reward-related cerebral activity. In Experiment 2, participants were instructed to press a key when hearing a non-voice pure tone and not give any response when they heard voice stimuli. In this task, no difference were found between the ERP to same-sex voices and that to opposite-sex voices, suggesting that the cerebral activity to opposite-sex voices may disappear without gender-related attention. These results provide significant implications on cognitive mechanisms with regard to opposite-sex specific voice processing.
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Noise provides new insights on contrast sensitivity function.
PLoS ONE
PUBLISHED: 01-01-2014
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Sensitivity to luminance difference, or contrast sensitivity, is critical for animals to survive in and interact with the external world. The contrast sensitivity function (CSF), which measures visual sensitivity to spatial patterns over a wide range of spatial frequencies, provides a comprehensive characterization of the visual system. Despite its popularity and significance in both basic research and clinical practice, it hasn't been clear what determines the CSF and how the factors underlying the CSF change in different conditions. In the current study, we applied the external noise method and perceptual template model to a wide range of external noise and spatial frequency (SF) conditions, and evaluated how the various sources of observer inefficiency changed with SF and determined the limiting factors underlying the CSF. We found that only internal additive noise and template gain changed significantly with SF, while the transducer non-linearity and coefficient for multiplicative noise were constant. The 12-parameter model provided a very good account of all the data in the 200 tested conditions (86.5%, 86.2%, 89.5%, and 96.4% for the four subjects, respectively). Our results suggest a re-consideration of the popular spatial vision model that employs the CSF as the front-end filter and constant internal additive noise across spatial frequencies. The study will also be of interest to scientists and clinicians engaged in characterizing spatial vision deficits and/or developing rehabilitation methods to restore spatial vision in clinical populations.
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Binocular combination of second-order stimuli.
PLoS ONE
PUBLISHED: 01-01-2014
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Phase information is a fundamental aspect of visual stimuli. However, the nature of the binocular combination of stimuli defined by modulations in contrast, so-called second-order stimuli, is presently not clear. To address this issue, we measured binocular combination for first- (luminance modulated) and second-order (contrast modulated) stimuli using a binocular phase combination paradigm in seven normal adults. We found that the binocular perceived phase of second-order gratings depends on the interocular signal ratio as has been previously shown for their first order counterparts; the interocular signal ratios when the two eyes were balanced was close to 1 in both first- and second-order phase combinations. However, second-order combination is more linear than previously found for first-order combination. Furthermore, binocular combination of second-order stimuli was similar regardless of whether the carriers in the two eyes were correlated, anti-correlated, or uncorrelated. This suggests that, in normal adults, the binocular phase combination of second-order stimuli occurs after the monocular extracting of the second-order modulations. The sensory balance associated with this second-order combination can be obtained from binocular phase combination measurements.
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Design, synthesis and cytotoxic activities of novel aliphatic amino-substituted flavonoids.
Molecules
PUBLISHED: 09-29-2013
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A series of flavonoids 9a-f, 13b, 13d, 13e and 14a-f bearing diverse aliphatic amino moieties were designed, synthesized and evaluated for their cytotoxic activities against the ECA-109, A-549, HL-60, and PC-3 cancer cell lines. Most of the compounds exhibited moderate to good activities. The structure-activity relationships were studied, revealing that the chalcone skeleton is the most preferable for cytotoxic activities. Chalcone 9d was the most promising compound due to its high potency against the examined cancer cell lines (its IC?? values against ECA-109, A549, HL-60 and PC-3 cells were 1.0, 1.5, 0.96 and 3.9 ?M, respectively).
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The effect of functional MAPKAPK2 copy number variation CNV-30450 on elevating nasopharyngeal carcinoma risk is modulated by EBV infection.
Carcinogenesis
PUBLISHED: 09-20-2013
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Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2) is recognized as oncogenic and simulative role on tumorigenesis by virtue of abnormal expression in cancer including nasopharyngeal carcinoma (NPC). We hypothesized that the copy number variation (CNV)-30450, which duplicates the MAPKAPK2 promoter, may affect MAPKAPK2 expression and be associated with NPC risk. In two independent case-control panels of southern and eastern Chinese with a total of 1590 NPC patients and 1979 cancer-free controls, we investigated the association between CNV-30450 and NPC risk by genotyping the CNV-30450 with the TaqMan assay, and tested its biological effect. Consistent findings were observed in the two populations, that the increased copy number of CNV-30450 was associated with increased risk of NPC (3/4-copy versus 2-copy: odds ratio = 1.28, 95% confidence interval = 1.10-1.49), in which lies a biological mechanism that the adverse genotypes enhanced the promoter activity of MAPKAPK2 and elevated MAPKAPK2 expression. Moreover, the CNV-30450 adverse genotypes significantly interacted with Epstein-Barr virus (EBV) infection on increasing NPC risk (P = 0.035), and the genotype-phenotype correlation was only significant in EBV-positive cases (P = 0.037) but not in EBV-negative ones (P = 0.366). These data suggest that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC. Summary: This case-control study suggests that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC.
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Tri-modal microscopy with multiphoton and optical coherence microscopy/tomography for multi-scale and multi-contrast imaging.
Biomed Opt Express
PUBLISHED: 09-01-2013
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Multi-scale multimodal microscopy is a very useful technique by providing multiple imaging contrasts with adjustable field of views and spatial resolutions. Here, we present a tri-modal microscope combining multiphoton microscopy (MPM), optical coherence microscopy (OCM) and optical coherence tomography (OCT) for subsurface visualization of biological tissues. The advantages of the tri-modal system are demonstrated on various biological samples. It enables the visualization of multiple intrinsic contrasts including scattering, two-photon excitation fluorescence (TPEF), and second harmonic generation (SHG). It also enables a rapid scanning over a large tissue area and a high resolution zoom-in for cellular-level structures on regions of interest. The tri-modal microscope can be important for label-free imaging to obtain a sufficient set of parameters for reliable sample analysis.
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A genetic polymorphism in lincRNA-uc003opf.1 is associated with susceptibility to esophageal squamous cell carcinoma in Chinese populations.
Carcinogenesis
PUBLISHED: 07-19-2013
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The development of esophageal squamous cell carcinoma (ESCC) is a multifactorial process, and associations between genetic variants and ESCC have been identified in genome-wide association studies. The aim of this study was to evaluate the effects of single nucleotide polymorphisms (SNPs) of long intergenic non-coding RNAs (lincRNAs) on ESCC susceptibility in Chinese populations. We scoured exons of lincRNAs located in ESCC susceptibility loci for all probable functional SNPs. These 52 SNPs were opted for and genotyped in 1493 ESCC patients and 1553 cancer-free controls from eastern and southern Chinese populations, and their associations with the risk for ESCC were estimated using logistic regression. Functional relevance was further examined by biochemical assays. Significant differences were found between patients and controls in the genotype frequencies for the rs11752942A>G site in the lincRNA-uc003opf.1 exon. Compared with the rs11752942AA genotype, AG and GG genotypes had a significantly reduced risk of ESCC (adjusted odds ratio = 0.73; 95% confidence interval = 0.63-0.84). Biochemical analysis demonstrated that, when compared with the A allele, the rs11752942G allele could markedly attenuate the level of lincRNA-uc003opf.1 both in vivo and in vitro by binding micro-RNA-149*, thereby affecting cell proliferation and tumor growth. These findings indicated that functional polymorphism rs11752942A>G in lincRNA-uc003opf.1 exon might be a genetic modifier for the development of ESCC.
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[Aging affects on the response irregularity of cells in different visual areas of cats].
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi
PUBLISHED: 07-18-2013
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In this research, we compared the visual neuron responses for LGN, A18 and PMLS of old and young cats with extracellular single-neuron recording techniques. We used firing rate vector to characterize information, and response irregularity of cells to evaluate the degeneration of visual characters. Response irregularity is characterized by means of the two coefficients of variation of firing rate vectors: Cv and Cv2. We found that there was no significant change of the response irregularity in LGN areas during the aging process from young to old cats. But in the other two areas, neurons of old cats exhibited significantly larger response irregularity than those of young cats. The result indicated that the information processing function of advanced visual cortex was impaired by aging. This result also provids a reference for the research of the other neuronal system changes during aging process.
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Functional polymorphisms in the CD44 gene and acute myeloid leukemia cancer risk in a Chinese population.
Mol. Carcinog.
PUBLISHED: 07-17-2013
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CD44 is such one adhesion molecule that mediates interactions between acute myeloid leukemia (AML) cells and stromal. It has been demonstrated that CD4 plays a critical role in AML development. However, studies of functional single nucleotide polymorphisms (SNPs) in CD44 gene have not touched upon AML. This case-control study probed the contribution of functional SNPs in CD44 gene to AML susceptibility in eastern Chinese population. Five representative SNPs of CD44 (rs10836347C>T, rs13347C>T, rs1425802A>G, rs11821102G>A, rs713330T>C) were opted and genotyped in 421 AML patients and 461 healthy subjects and the association with risk of AML was estimated by logistic regression. Moreover, the potential role of rs13347C>T in AML was further explored. Compared with the rs13347CC genotype, CT carriers had a significant increase in AML susceptibility (adjusted odds ratio [OR]?=?1.76; 95% confidence interval [CI]?=?1.32-2.34), TT carriers had a further increased risk of AML (OR?=?2.67; 95% CI?=?1.69-4.21). Furthermore, our transient transfection assay and Western blot results demonstrated that the presence of rs13347T allele led to more CD44 expression. Yet, there exists no significant difference in genotype frequencies of the other four sites between cases and controls. Above findings suggest that rs13347C>T in 3UTR of CD44 may be a genetic modifier for developing AML. © 2013 Wiley Periodicals, Inc.
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Contrast gain-control in stereo depth and cyclopean contrast perception.
J Vis
PUBLISHED: 07-04-2013
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Although human observers can perceive depth from stereograms with considerable contrast difference between the images presented to the two eyes (Legge & Gu, 1989), how contrast gain control functions in stereo depth perception has not been systematically investigated. Recently, we developed a multipathway contrast gain-control model (MCM) for binocular phase and contrast perception (Huang, Zhou, Lu, & Zhou, 2011; Huang, Zhou, Zhou, & Lu, 2010) based on a contrast gain-control model of binocular phase combination (Ding & Sperling, 2006). To extend the MCM to simultaneously account for stereo depth and cyclopean contrast perception, we manipulated the contrasts (ranging from 0.08 to 0.4) of the dynamic random dot stereograms (RDS) presented to the left and right eyes independently and measured both disparity thresholds for depth perception and perceived contrasts of the cyclopean images. We found that both disparity threshold and perceived contrast depended strongly on the signal contrasts in the two eyes, exhibiting characteristic binocular contrast gain-control properties. The results were well accounted for by an extended MCM model, in which each eye exerts gain control on the other eyes signal in proportion to its own signal contrast energy and also gain control over the other eyes gain control; stereo strength is proportional to the product of the signal strengths in the two eyes after contrast gain control, and perceived contrast is computed by combining contrast energy from the two eyes. The new model provided an excellent account of our data (r(2) = 0.945), as well as some challenging results in the literature.
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A functional polymorphism in the promoter of ERK5 gene interacts with tobacco smoking to increase the risk of lung cancer in Chinese populations.
Mutagenesis
PUBLISHED: 06-26-2013
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Mitogen/extracellular signal-regulated kinase-5 (MEK5)/extracellular signal-regulated protein kinase-5 (ERK5) pathway plays a pro-oncogenic role in tumourigenesis by anticell apoptosis, promoting cell proliferation and differentiation in response to extracellular stimuli. As overexpressed MEK5/ERK5 is involved in the development of lung cancer, we hypothesised that the single nucleotide polymorphisms (SNPs) in MEK5 and ERK5 genes may influence gene expression and thus be associated with lung cancer risk. Five putative functional polymorphisms (rs3743353T>C, rs7172582C>T and rs2278076A>G of MEK5 and rs3866958G>T and rs2233083C>T of ERK5) were genotyped in two independent case-control studies with a total of 1559 lung cancer patients and 1679 controls in southern and eastern Chinese population. We found the rs3866958G>T of ERK5 was significantly associated with lung cancer risk, while other SNPs were not. Compared with the rs3866958TG/TT genotypes, the GG genotype conferred an increased risk of lung cancer (odds ratio = 1.30, 95% confidence interval = 1.12-1.51, P = 5.0×10(-4)), and this effect was more pronounced in smokers, accompanying with a significant interaction with smoking (P interaction = 0.013). The GG genotype also had significant higher mRNA levels of ERK5 in lung cancer tissues than TG/TT genotypes (P = 1.0×10(-4)); the luciferase reporter with the G allele showed significant higher transcription activities than the T allele, especially after the treatment with tobacco extract in vitro. Our data indicated that the functional polymorphism rs3866958G>T in ERK5 was associated with an increased lung cancer risk in smokers by virtue of the positive interaction with smoking on promoting the ERK5 expression, which might be a valuable indicator for predicting lung cancer risk in smokers.
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A sequence polymorphism in miR-608 predicts recurrence after radiotherapy for nasopharyngeal carcinoma.
Cancer Res.
PUBLISHED: 06-24-2013
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Nasopharyngeal carcinoma is treated with radiotherapy and other modalities, but there is little information on individual genetic factors to help predict and improve patient outcomes. Single-nucleotide polymorphisms (SNP) in mature microRNA (miRNA) sequences have the potential to exert broad impact as miRNAs target many mRNAs. The aim of this study was to evaluate the effects of SNPs in mature miRNA sequences on clinical outcome in patients with nasopharyngeal carcinoma receiving radiotherapy. In particular, we analyzed associations between seven SNPs and nasopharyngeal carcinoma locoregional recurrence (LRR) in 837 patients from eastern China, validating the findings in an additional 828 patients from southern China. We found that miR-608 rs4919510C > G exhibited a consistent association with LRR in the discovery set [HR, 2.05; 95% confidence interval (CI), 1.35-3.21], the validation set (HR, 2.24; 95% CI, 1.45-3.38), and the combined dataset (HR, 2.08; 95% CI, 1.41-3.26). Biochemical investigations showed that rs4919510C > G affects expression of miR-608 target genes along with nasopharyngeal carcinoma cell growth after irradiation in vivo and in vitro. Notably, X-ray radiation induced more chromatid breaks in lymphocyte cells from rs4919510CC carriers than in those from subjects with other genotypes (P = 0.0024). Our findings reveal rs4919510C > G in miR-608 as a simple marker to predict LRR in patients with radiotherapy-treated nasopharyngeal carcinoma.
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Transfer in motion perceptual learning depends on the difficulty of the training task.
J Vis
PUBLISHED: 06-11-2013
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One hypothesis in visual perceptual learning is that the amount of transfer depends on the difficulty of the training and transfer tasks (Ahissar & Hochstein, 1997; Liu, 1995, 1999). Jeter, Dosher, Petrov, and Lu (2009), using an orientation discrimination task, challenged this hypothesis by arguing that the amount of transfer depends only on the transfer task but not on the training task. Here we show in a motion direction discrimination task that the amount of transfer indeed depends on the difficulty of the training task. Specifically, participants were first trained with either 4° or 8° direction discrimination along one average direction. Their transfer performance was then tested along an average direction 90° away from the trained direction. A variety of transfer measures consistently demonstrated that transfer performance depended on whether the participants were trained on 4° or 8° directional difference. The results contradicted the prediction that transfer was independent of the training task difficulty.
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A microRNA-135a/b binding polymorphism in CD133 confers decreased risk and favorable prognosis of lung cancer in Chinese by reducing CD133 expression.
Carcinogenesis
PUBLISHED: 05-28-2013
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CD133 is a pivotal marker of cancer stem cells (CSCs), which is involved in tumorigenesis and cancer progression. Recent studies have identified CD133 to be a prognostic factor for cancer rested with its expression and genetic variants. Here, we hypothesized that the single nuclear polymorphisms (SNPs) in CD133 may be associated with lung cancer risk and prognosis. Based on three independent case-control analyses with a total of 2332 lung cancer cases and 2457 controls, the gene-based association analysis with 13 polymorphisms of CD133 suggested that CD133 is a susceptible gene for lung cancer (P = 0.043) and that the SNP rs2240688A>C in the 3-untranslated region of CD133 is the most significant associated SNP with the risk of lung cancer (P = 0.020); further analysis showed that the rs2240688C variant genotypes (CA+CC) harbored a decreased risk of lung cancer (odds ratio = 0.80; 95% confidence interval (CI) = 0.72-0.90) and conferred a favorable survival for lung cancer patients (median survival time: 15 months) compared with AA genotype (median survival time: 11 months, log-rank test: P = 3.31 × 10(-6); Cox model: hazards ratio = 0.81, 95% CI = 0.70-0.94). Functional assays revealed that the rs2240688A to rs2240688C transition gained a new binding of the microRNA hsa-miR-135a/b and decreased the CD133 expression. Our data suggest that the functional polymorphism rs2240688A>C in CD133 is associated with lung cancer risk and survival. This SNP may be a functional biomarker to predict risk and prognosis of lung cancer.
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ST-T-wave alternans in Brugada electrocardiogram type I pattern during the resolution of febrile states.
Cardiovasc J Afr
PUBLISHED: 04-25-2013
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Brugada syndrome is often electrocardiographically characterised by ST-segment elevation in the right precordial leads. The characteristic Brugada electrocardiogram pattern is often dynamic and concealed, and may be revealed during febrile states or under the challenge of drugs that have a sodium channel-blocking effect. In this report, we describe two cases of exposure of the Brugada electrocardiogram pattern during febrile states. When the patients body temperature decreased and before the ST-elevation disappeared, ST-segment and T-wave alternans in the right precordial leads were observed, especially in lead V2.
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Genome-wide association study identifies common variants in SLC39A6 associated with length of survival in esophageal squamous-cell carcinoma.
Nat. Genet.
PUBLISHED: 04-12-2013
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We conducted a genome-wide scan of SNPs to identify variants associated with length of survival in 1,331 individuals with esophageal squamous-cell carcinoma (ESCC), with associations validated in 2 independent sets including 1,962 individuals with this cancer. We identified rs1050631 in SLC39A6 as associated with the survival times of affected individuals, with the hazard ratio for death from ESCC in the combined sample being 1.30 (95% confidence interval (CI) = 1.19-1.43; P = 3.77 × 10(-8)). rs7242481, located in the 5 UTR of SLC39A6, disturbs a transcriptional repressor binding site and results in upregulation of SLC39A6 expression. Immunohistochemical staining of ESCC tissues showed that higher expression of SLC39A6 protein was correlated with shorter length of survival in individuals with advanced ESCC (P = 0.013). Knockdown of SLC39A6 expression suppressed proliferation and invasion in ESCC cells. These results suggest that SLC39A6 has an important role in the prognosis of ESCC and may be a potential therapeutic target.
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ERCP in acute cholangitis during third trimester of pregnancy.
Hepatogastroenterology
PUBLISHED: 02-22-2013
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To explore the efficacy and safety of modified endoscopic retrograde cholangiopancreatographies (ERCP) management of acute cholangitis during the third trimester of pregnancy.
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Heterozygous genetic variations of FOXP3 in Xp11.23 elevate breast cancer risk in Chinese population via skewed X-chromosome inactivation.
Hum. Mutat.
PUBLISHED: 01-22-2013
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FOXP3 (forkhead box P3: also known as IPEX, XPID) is not only a hallmark of immunosuppressive regulatory T cells (Tregs), but also an X-linked breast cancer suppressor gene expressed in tumor cells. A two-stage investigation was conducted in individuals from northern, southern and eastern China. Individuals carrying a FOXP3 rs2294021CT genotype showed about 1.5-fold increased risk of breast cancer compared with TT carriers. In a related biochemical assay, the rs2294021C allele was found to significantly enhance transcription activity, leading to higher mRNA levels of FOXP3 compared with T allele. Moreover, the number of Tregs and its corresponding interleukin-10 (IL-10) secretion were elevated whereas the proliferation of antitumor T cells was decreased in the C-allele carriers. The breast cancer oncogenes Her-2/ErbB2 and Skp2 were also found to be significantly inhibited in C-allele carriers. Moreover, skewed X-chromosome inactivation (SXCI) analysis showed that rs2294021CT carriers with SXCI showed higher risk than the homozygous carriers and CT carriers without SXCI, suggesting a possible interaction between the rs2294021CT genotype and SXCI. Taken together, these findings indicate that the rs2294021CT genotype may increase an individuals susceptibility to breast cancer by breaking the balance between Treg-mediated immune tolerance and FOXP3-controlled tumor-suppressive effect.
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A functional copy number variation in the WWOX gene is associated with lung cancer risk in Chinese.
Hum. Mol. Genet.
PUBLISHED: 01-22-2013
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WW domain-containing oxidoreductase (WWOX) is a tumor suppressor that has been reported to lose function due to genetic alterations in several cancers. WWOX maps to the common chromosomal fragile site FRA16D and several copy number variations (CNVs) were found within this gene. In this study, we investigated the association between the CNVs of WWOX and lung cancer risk in four independent case-control studies, which are on 2942 lung cancer cases and 3074 cancer-free controls of southern, eastern and northern Chinese. A common CNV-67048 was genotyped by the Taqman real-time PCR, and its biological effect was accessed with protein expression and sequencing assays. We found that in comparison with the common 2-copy genotype, the carriers of loss variant genotypes (1-copy or 0-copy) had a significantly increased risk of lung cancer (adjusted OR = 1.39, 95% CI = 1.24-1.55, P = 9.01×10(-9)) in a dose-response manner (Ptrend = 1.12 × 10(-10)), and the WWOX protein expressions in lung cancer tissues were significantly lower (P = 0.036), accompanying a higher rate of exons absence (P = 0.021) in subjects with loss genotypes of CNV-67048. Our data suggest that the loss genotypes of CNV-67048 in WWOX predispose their carriers to lung cancer; this might be related with altered WWOX gene expression and exons absence in them.
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The case-only test for gene-environment interaction is not uniformly powerful: an empirical example.
Genet. Epidemiol.
PUBLISHED: 01-14-2013
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The case-only test has been proposed as a more powerful approach to detect gene-environment (G × E) interactions. This approach assumes that the genetic and environmental factors are independent. Although it is well known that Type I error rate will increase if this assumption is violated, it is less widely appreciated that G × E correlation can also lead to power loss. We illustrate this phenomenon by comparing the performance of the case-only test to other approaches to detect G × E interactions in a genome-wide association study (GWAS) of esophageal squamous-cell carcinoma (ESCC) in Chinese populations. Some of these approaches do not use information on the correlation between exposure and genotype (standard logistic regression), whereas others seek to use this information in a robust fashion to boost power without increasing Type I error (two-step, empirical Bayes, and cocktail methods). G × E interactions were identified involving drinking status and two regions containing genes in the alcohol metabolism pathway, 4q23 and 12q24. Although the case-only test yielded the most significant tests of G × E interaction in the 4q23 region, the case-only test failed to identify significant interactions in the 12q24 region which were readily identified using other approaches. The low power of the case-only test in the 12q24 region is likely due to the strong inverse association between the single nucleotide polymorphism (SNPs) in this region and drinking status. This example underscores the need to consider multiple approaches to detect G × E interactions, as different tests are more or less sensitive to different alternative hypotheses and violations of the G × E independence assumption.
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Identification of common variants in BRCA2 and MAP2K4 for susceptibility to sporadic pancreatic cancer.
Carcinogenesis
PUBLISHED: 01-08-2013
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Germline mutations in genes that cause hereditary syndromes are highly predisposed to familial pancreatic cancer. However, genetic susceptibility to sporadic pancreatic cancer is largely uncovered. We conducted a two-stage association study on pancreatic cancer that included 981 cases and 1991 controls in the first stage followed by a second stage (2603 cases and 2877 controls). Using an approach based on candidate genes whose roles in pancreatic cancer have been well known, we identified two new susceptibility loci. rs11571836 located in the BRCA2 3-untranslated region was significantly associated with lower expression of BRCA2 transcript and increased pancreatic cancer risk [odds ratio = 1.30, 95% confidence interval = 1.14-1.47, P = 7.64 × 10(-5)] in a recessive manner. rs12939944 located in the MAP2K4 intron was associated with decreased risk (odds ratio = 0.82, 95% confidence interval = 0.74-0.91, P = 0.0001) in a dominant manner. Our results demonstrate for the first time that common variants in BRCA2 and MAP2K4 are susceptibility to sporadic pancreatic cancer.
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Sipa1 promoter polymorphism predicts risk and metastasis of lung cancer in Chinese.
Mol. Carcinog.
PUBLISHED: 01-07-2013
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Signal-induced proliferation associated gene 1 (Sipa1) is a signal transducer to activate the Ras-related proteins and modulate cell progression, differentiation, adhesion and cancer metastasis. In this study, we tested the hypothesis that single nucleotide polymorphisms (SNPs) in Sipa1 are associated with lung cancer risk and metastasis. Three common SNPs (rs931127A > G, rs2448490G > A, and rs3741379G > T) were genotyped in a discovery set of southern Chinese population and then validated the promising SNPs in a validation set of an eastern Chinese population in a total of 1559 lung cancer patients and 1679 cancer-free controls. The results from the two sets were consistent, the rs931127GG variant genotype had an increased risk of lung cancer compared to the rs931127AA/GA genotypes (OR = 1.27; 95% CI = 1.09-1.49) after combination of the two populations, and the rs931127GG interacted with pack-year smoked on increasing lung cancer risk (P = 0.037); this SNP also had an effect on patients clinical stages (P = 0.012) that those patients with the rs931127GG genotype had a significant higher metastasis rate and been advanced N, M stages at diagnosis. However, these associations were not observed for rs2448490G > A and rs3741379G > T in the discovery set. Our data suggest that the SNP rs931127A > G in the promoter of Sipa1 was significantly associated with lung cancer risk and metastasis, which may be a biomarker to predict the risk and metastasis of lung cancer.
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IL-21 gene polymorphism is associated with the prognosis of breast cancer in Chinese populations.
Breast Cancer Res. Treat.
PUBLISHED: 01-04-2013
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Interleukin (IL)-21, which is secreted by activated CD4(+) T cells and NKT cells, has been found to be able to influence the humoral and cell-mediated immune responses and have potent antitumor activity in animal models. This study was to investigate the impact of genetic polymorphisms in IL-21 on survival of breast cancer. Four TagSNPs of IL-21 (rs12508721C>T, rs907715G>A, rs13143866G>A, rs2221903A>G) were selected and then genotyped in 891 patients with breast cancer in Eastern and Southern Chinese populations. We then examined the associations between these SNPs and overall survival. Potential function of rs12508721C>T and association between this variation and breast cancer prognosis were further studied. Overall, 121 of the patients had died over the followed-up period of 5 years. The IL-21 rs12508721T allele predicted longer five-year survival (HR = 0.347, 95 % CI = 0.187-0.644, P < 0.0001) in the discovery cohort, the independent validation cohort (HR = 0.429, 95 % CI = 0.244-0.755, P = 0.012), and combined group (HR = 0.447, 95 % CI = 0.301-0.667, P < 0.0001). Furthermore, our luciferase assay revealed that rs12508721T variant allele had a higher transcription activity and the RT-PCR and ELISA assay showed that rs12508721 variant genotypes (CT and TT) carriers have more IL-21 expression than CC carriers (P < 0.05). Our present study established a robust association between the functional polymorphism (rs12508721C>T) in IL-21 and prognosis of breast cancer, indicating that this polymorphism may be a potential biomarker for prognosis of breast cancer.
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Functional polymorphisms in NF?B1/I?B? predict risks of chronic obstructive pulmonary disease and lung cancer in Chinese.
Hum. Genet.
PUBLISHED: 01-03-2013
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Lung inflammation is the major pathogenetic feature for both chronic obstructive pulmonary disease (COPD) and lung cancer. The nuclear factor-kappa B (NF?B) and its inhibitor (I?B) play crucial roles in inflammatory. Here, we tested the hypothesis that single nucleotide polymorphisms (SNPs) in NF?B/I?B confer consistent risks for COPD and lung cancer. Four putative functional SNPs (NF?B1: -94del>insATTG; NF?B2: -2966G>A; I?B?: -826C>T, 2758G>A) were analyzed in southern and validated in eastern Chineses to test their associations with COPD risk in 1,511 COPD patients and 1,677 normal lung function controls, as well as lung cancer risk in 1,559 lung cancer cases and 1,679 cancer-free controls. We found that the -94ins ATTG variants (ins/del + ins/ins) in NF?B1 conferred an increased risk of COPD (OR 1.27, 95% CI 1.06-1.52) and promoted COPD progression by accelerating annual FEV1 decline (P = 0.015). The 2758AA variant in I?B? had an increased risk of lung cancer (OR 1.53, 95% CI 1.30-1.80) by decreasing I?B? expression due to the modulation of microRNA hsa-miR-449a but not hsa-miR-34b. Furthermore, both adverse genotypes exerted effect on increasing lung cancer risk in individuals with pre-existing COPD, while the -94del>insATTG did not in those without pre-existing COPD. However, no significant association with COPD or lung cancer was observed for -2966G>A and -826C>T. Our data suggested a common susceptible mechanism of inflammation in lung induced by genetic variants in NF?B1 (-94del>ins ATTG) or I?B? (2758G>A) to predict risk of COPD or lung cancer.
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NBS1 rs1805794G>C polymorphism is associated with decreased risk of acute myeloid leukemia in a Chinese population.
Mol. Biol. Rep.
PUBLISHED: 01-03-2013
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As a key encoding protein gene of MRN (MRE11-RAD50-NBS1) complex, NBS1 plays a crucial role in maintaining genomic stability and preventing cell apoptosis, inflammation and tumorgenesis. Single nucleotide polymorphisms (rs2735383 and rs1805794) in NBS1 have been frequently studied in some cancers with discordant results in previous case-control studies. However, the relationship between these two functional polymorphisms and the susceptibility to acute myeloid leukemia (AML) in Chinese population has not been investigated. We performed a case-control study with 428 patients and 600 controls to detect the association between the two polymorphisms of NBS1 and the risk of AML in a Chinese population. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was carried out to determine the genotypes of potential functional SNPs in NBS1 gene. The results showed that compared with the homozygous carriers rs1805794CC, rs1805794GC genotype was significantly associated with decreased risk of AML in total subjects (adjusted odds ratio (OR) = 0.50; 95% CI = 0.37-0.67), the risk decreased even further in those carrying rs1805794GG genotype (OR = 0.23; 95% CI = 0.16-0.34). No significant association was found between rs2735383C>G polymorphism and the risk of AML (OR = 0.93; 95% CI = 0.71-1.22 for GC; OR = 0.78; 95% CI = 0.53-1.13 for CC, P = 0.152). These findings indicated that rs1805794G/C polymorphism in NBS1 may play a protective role in mediating the risk of AML.
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Functional Genetic Polymorphisms in PP2A Subunit Genes Confer Increased Risks of Lung Cancer in Southern and Eastern Chinese.
PLoS ONE
PUBLISHED: 01-01-2013
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Protein phosphatase-2A (PP2A) is one of the major cellular serine-threonine phosphatases and functions as a tumor suppressor that negatively regulates the activity of some oncogenic kinases. Recent studies have reported that PP2A expression was suppressed during lung carcinogenesis, we there hypothesized that the single nucleotide polymorphisms (SNPs) in PP2A subunit genes may affect PP2A function and thus contribute to lung cancer susceptibility. In a two-stage case-control study with a total of 1559 lung cancer patients and 1679 controls, we genotyped eight putative functional SNPs and one identified functional SNP (i.e., rs11453459) in seven major PP2A subunits (i.e., PPP2R1A, PPP2R1B, PPP2CA, PPP2R2A, PPP2R2B, PPP2R5C, PPP2R5E) in southern and eastern Chinese. We found that rs11453459G (-G/GG) variant genotypes of PPP2R1A and the rs1255722AA variant genotype of PPP2R5E conferred increased risks of lung cancer (rs11453459, -G/GG vs. -: OR?=?1.31, 95% CI?=?1.13-1.51; rs1255722, AA vs.
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Multiscale multimodal imaging with multiphoton microscopy and optical coherence tomography.
Opt Lett
PUBLISHED: 12-20-2011
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A multiscale multiphoton microscopy (MPM) and optical coherence tomography (OCT) system has been developed using a sub-10 fs Ti:sapphire laser. The system performs cross-sectional OCT imaging over millimeter field-of-view and en-face high-resolution MPM imaging with submicrometer resolution from the same sample location. With fish cornea, we have demonstrated cross-sectional imaging of cornea tissue layers using OCT, and the zoom-in imaging of cells and collagen fibers in each layer using MPM. The multiscale MPM/OCT system shows the potential of a rapid coarse scan to search for abnormal regions and the subsequent fine zoom-in imaging for diagnosis.
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A functional polymorphism at microRNA-629-binding site in the 3-untranslated region of NBS1 gene confers an increased risk of lung cancer in Southern and Eastern Chinese population.
Carcinogenesis
PUBLISHED: 11-22-2011
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The genetic variations in NBS1 gene have been reported to be associated with cancer risk. The polymorphisms in 3-untranslated region (3-UTR) of NBS1 might affect genes function and thus contribute to cancer susceptibility. We hypothesized that these polymorphisms of NBS1 are associated with the lung cancer risk. In two independent case-control studies conducted in Southern and Eastern Chinese, we genotyped three tagSNPs (rs14448, rs13312986 and rs2735383) in Southern Chinese and then validated the discovered association in Eastern Chinese. No significant association was observed for rs13312986 and rs14448; we only found that the rs2735383CC genotype had a significantly increased risk of lung cancer under a recessive genetic model in the total 1559 cases versus 1679 controls (odds ratio = 1.40, 95% confidence interval = 1.18-1.66, P = 0.0001) when compared with GG or GC genotypes; the rs2735383CC genotype carriers had lower messenger RNA and protein expression levels in tumor tissues than those of other genotypes as quantitative polymerase chain reaction and western blot shown. Luciferase assay revealed that the rs2735383C allele had a lower transcription activity than G allele, and the hsa-miR-629 but not hsa-miR-499-5P had effect on modulation of NBS1 gene in vitro. We further observed that the X-ray radiation induced more chromatid breaks in lymphocyte cells from the carriers of rs2735383CC homozygote than those from the subjects with other genotypes (P = 0.0008). Our data suggested that the rs2735383G>C variation contributes to an increased risk of lung cancer by diminishing genes expression through binding of microRNA-629 to the polymorphic site in the 3-UTR of NBS1 gene.
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Association between the p73 exon 2 G4C14-to-A4T14 polymorphism and cancer risk: a meta-analysis.
DNA Cell Biol.
PUBLISHED: 10-19-2011
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The TP53 homolog p73 is structurally and functionally similar to TP53 and plays an important role in modulating cell-cycle control, apoptosis, and cell growth. G4C14-to-A4T14 is the most commonly studied polymorphism of this gene for its association with risk of cancers, but the results are confusing rather than conclusive. We performed a meta-analysis using 21 eligible studies with a total of 7581 patients and 10,413 controls to summarize the data for an association between the p73 G4C14-to-A4T14 polymorphism and cancer risk. Compared with the common GC/GC genotype, the AT carriers (AT/GC, AT/AT) had a 1.18-fold elevated risk of cancer (95% confidence interval [CI]=1.11-1.25, p<0.00001) in a dominant genetic model as estimated in a fixed effect model. The effect of the G4C14-to-A4T14 polymorphism was further evaluated through stratification analysis. In four lung cancer studies, the variant genotypes had a significantly increased risk of lung cancer (odds ratio [OR]=1.16, 95% CI=1.04-1.28, p=0.005). Similar phenomena were also found in two squamous cell carcinoma of the head and neck studies (OR=1.32, 95% CI=1.12-1.56, p=0.0010), two oral cancer studies (OR=1.57, 95% CI=1.26-1.95, p<0.0001), and three colorectal cancer studies (OR=1.23, 95% CI=1.01-1.50, p=0.04). Increased risk of cancer associated with G4C14-to-A4T14 variant genotypes was pronounced in Caucasians (OR=1.21, 95% CI=1.11-1.31, p<0.00001), the Japanese population (OR=1.24, 95% CI=1.01-1.52, p=0.04), and the Korean population (OR=1.27, 95% CI=1.07-1.52, p=0.007). Our meta-analysis suggests that the p73 G4C14-to-A4T14 polymorphism genotypes (GC/AT+AT/AT) may be associated with an increased risk of cancer in most cancer types and ethnicities.
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Functional genetic variations of cyclooxygenase-2 and susceptibility to acute myeloid leukemia in a Chinese population.
Eur. J. Haematol.
PUBLISHED: 08-19-2011
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Cyclooxygenase-2 (COX-2) is a key enzyme involved in the synthesis of prostaglandins, which are known to play important roles in the proliferation and differentiation of leukemia cells, and inhibitors of COX-2 can suppress the proliferation and differentiation of human leukemia cell lines. Single-nucleotide polymorphisms (-765G/C: rs20417, -1195A/G: rs689466, and -1290A/G: rs689465) in the COX-2 promoter might contribute to differential COX-2 expression and subsequent interindividual variability in susceptibility to cancer.
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Contrast adaptation in cat lateral geniculate nucleus and influence of corticothalamic feedback.
Eur. J. Neurosci.
PUBLISHED: 07-12-2011
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Contrast adaptation is a basic property of visual information processing. However, important questions about contrast adaptation in the lateral geniculate nucleus (LGN) remain. For example, it is unclear whether the different information channels have the same or distinct contrast adaptation properties and mechanisms. It has been recognized that the visual system is not a one-way ascending pathway, but also contains descending feedback projections. Although studies have explored the role of this feedback system, it is unclear whether corticothalamic feedback contributes to adaptation in the LGN. To investigate these questions, we studied contrast adaptation of LGN neurons in anesthetized and paralysed cats by measuring electrophysiological responses to visual test stimuli before and after adaptation induced by prolonged visual stimulation. After adaptation, contrast response functions were usually shifted towards higher contrasts, indicating decreased contrast gain, and the maximum response decreased. Also, contrast adaptation effects were stronger in Y-cells than in X-cells. Furthermore, adaptation effects were still observed in the LGN when the corticothalamic feedback was inactivated. Changes in the contrast gain of Y-cells were diminished in the absence of feedback, while contrast gain was largely unchanged in X-cells. Our observations confirm that contrast adaptation occurs in LGN neurons and furthermore demonstrate that Y-cells show stronger adaptation effects than X-cells. These results also provide an example of how corticothalamic feedback modulates contrast information processing distinctly in different information channels.
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A genome-wide association study identifies new susceptibility loci for non-cardia gastric cancer at 3q13.31 and 5p13.1.
Nat. Genet.
PUBLISHED: 06-07-2011
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Gastric cancer, including the cardia and non-cardia types, is the second leading cause of cancer-related deaths worldwide. To identify genetic risk variants for non-cardia gastric cancer, we performed a genome-wide association study in 3,279 individuals (1,006 with non-cardia gastric cancer and 2,273 controls) of Chinese descent. We replicated significant associations in an additional 6,897 subjects (3,288 with non-cardia gastric cancer and 3,609 controls). We identified two new susceptibility loci for non-cardia gastric cancer at 5p13.1 (rs13361707 in the region including PTGER4 and PRKAA1; odds ratio (OR) = 1.41; P = 7.6 × 10(-29)) and 3q13.31 (rs9841504 in ZBTB20; OR = 0.76; P = 1.7 × 10(-9)). Imputation analyses also confirmed previously reported associations of rs2294008 and rs2976392 on 8q24, rs4072037 on 1q22 and rs13042395 on 20p13 with non-cardia gastric cancer susceptibility in the Han Chinese population.
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Functional variant (-1304T>G) in the MKK4 promoter is associated with decreased risk of acute myeloid leukemia in a southern Chinese population.
Cancer Sci.
PUBLISHED: 05-25-2011
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As a member of the MAPK kinase family, mitogen-activated protein kinase kinase (MKK) 4 (NM_003010.2) is know to be involved in the regulation of apoptosis, inflammation, and tumorigenesis. Several polymorphisms have been identified in the promoter region of the MKK4 gene and we hypothesized that genetic variations in this region may alter gene expression, and thus cancer risk. In the present study, we genotyped two polymorphisms in the promoter of the MKK4 gene, namely -1304T>G (rs3826392) and -1044A>T (rs3809728), in 433 patients with AML and 600 controls, and assessed the association between those polymorphisms and the risk of AML. Compared with the -1304TT genotype, patients with the -1304TG genotype had a significantly decreased risk of AML (adjusted odds ratio (OR) 0.67; 95% confidence interval (CI) 0.51-0.87), with the risk decreased even further in those carrying -1304GG (OR 0.56; 95% CI 0.31-0.97). Additional experiments, which focused on reporter gene expression driven by MKK4 promoters, demonstrated that the presence of a -1304G allele led to greater transcriptional activity than the presence of a -1304T allele. However, no significant association was observed between the MKK4-1044A>T polymorphism and the risk of AML. These findings suggest that the functional -1304G>T variant may contribute to the risk of AML by enhancing the transcriptional activity of MKK4. Thus, this polymorphism may be a genetic modifier for the development of AML.
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Genome-wide association study identifies three new susceptibility loci for esophageal squamous-cell carcinoma in Chinese populations.
Nat. Genet.
PUBLISHED: 05-06-2011
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Esophageal squamous-cell carcinoma (ESCC) is one of the most prevalent cancers worldwide and occurs at a relatively high frequency in China. To identify genetic susceptibility loci for ESCC, we conducted a genome-wide association study on 2,031 individuals with ESCC (cases) and 2,044 controls of Chinese descent using 666,141 autosomal SNPs. We evaluated promising associations in an additional 6,276 cases and 6,165 controls of Chinese descent from different areas of China. We identified seven susceptibility loci on chromosomes 5q11, 6p21, 10q23, 12q24 and 21q22 (ranging from P = 7.48 × 10(-12) to P = 2.44 × 10(-31)); among these loci, 5q11, 6p21 and 21q22 were newly identified. Three variants in high linkage disequilibrium on 12q24 confer their risks to ESCC in a gene-lifestyle interaction manner, with more pronounced risk enhancement seen in tobacco and alcohol users. Furthermore, the identified variants had a cumulative association with ESCC risk (P(trend) = 7.92 × 10(-56)). These findings highlight the involvement of multiple genetic loci and gene-environment interaction in the development of esophageal cancer.
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Screening SNPs residing in the microRNA-binding sites of hepatocellular carcinoma related genes.
Int J Data Min Bioinform
PUBLISHED: 04-16-2011
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Single nucleotide polymorphisms located at miRNA-binding sites are likely to affect the expression of the miRNA targets and may contribute to the susceptibility of humans to common diseases. Here we selected 289 candidate Hepatocellular Carcinoma (HCC) related genes according to the existing literature and database. We identified putative miRNA-binding sites of 52 genes by specialised algorithms, screened SNPs in the 3-UTRs of 50 genes. Using BLAST program, we identified 5 genes that had SNPs in the regions of miRNA-binding sites, one of which is confirmed in another published study. We propose these SNPs for further investigations in case-control association studies.
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Genetic variations in CD14 promoter and acute lymphoblastic leukemia susceptibility in a Chinese population.
DNA Cell Biol.
PUBLISHED: 04-10-2011
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Recent findings suggest that CD14 may play a role in tumor development. Previous case-control studies have revealed that CD14 -260C/T and -651?C/T polymorphisms contribute to the risk of human diseases. However, the relationship between these two functional polymorphisms and susceptibility to acute lymphoblastic leukemia (ALL) has not been explored. In this study, we performed a case-control study in a Chinese population. We found that an increased risk of ALL was associated with the -260?TT (odds ratio [OR]=1.85, 95% confidence interval [CI]=1.26-2.63) genotype compared with the CT or CC genotype. No significant association was found between -651?CC genotype and ALL (OR=1.13, 95% CI=0.77-1.69). Moreover, the increased risk was only associated with the -260?TT genotype in B-ALL (OR=1.99, 95% CI=1.34-3.01) but not in T-ALL (OR=1.48, 95% CI=0.79-2.84). The findings suggest that CD14-260C/T polymorphism can contribute to B-ALL risk in a Chinese population.
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Genome-wide association study identifies five loci associated with susceptibility to pancreatic cancer in Chinese populations.
Nat. Genet.
PUBLISHED: 04-06-2011
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Pancreatic cancer has the lowest survival rate among human cancers, and there are no effective markers for its screening and early diagnosis. To identify genetic susceptibility markers for this cancer, we carried out a genome-wide association study on 981 individuals with pancreatic cancer (cases) and 1,991 cancer-free controls of Chinese descent using 666,141 autosomal SNPs. Promising associations were replicated in an additional 2,603 pancreatic cancer cases and 2,877 controls recruited from 25 hospitals in 16 provinces or cities in China. We identified five new susceptibility loci at chromosomes 21q21.3, 5p13.1, 21q22.3, 22q13.32 and 10q26.11 (P = 2.24 × 10(-13) to P = 4.18 × 10(-10)) in addition to 13q22.1 previously reported in populations of European ancestry. These results advance our understanding of the development of pancreatic cancer and highlight potential targets for the prevention or treatment of this cancer.
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Functional NBS1 polymorphism is associated with occurrence and advanced disease status of nasopharyngeal carcinoma.
Mol. Carcinog.
PUBLISHED: 03-23-2011
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As a component of the MRN (MRE11/RAD50/NBS1) complex, NBS1 plays an important role in cellular response to DNA damage and the maintenance of chromosomal integrity. The NBS1 E185Q polymorphism (8360G>C, rs1805794) has been frequently studied in some cancers with discordant results, but its association with nasopharyngeal carcinoma (NPC) in Chinese population has not been investigated. Moreover, there is no report about the association between NBS1 3UTR variant rs2735383 and the risk of NPC. A multiple center case-control analysis was performed to assess the association between NBS1 polymorphisms and NPC risk in Eastern and Southern Chinese population. The genotypes and haplotypes were determined in 1052 cases and 1168 controls and the associations with risk of NPC were estimated by logistic regression. Cell migration assays were performed in 24-well transwell chambers to detect the effects of NBS1 E185Q SNP on cell migration. We observed significant difference in genotype frequencies at the rs1805794 C/G site between cases and controls (P(trend) < 0.0001). The C allele increases the risk for invasive disease or metastatic disease, compared with G allele. More over, CNE-2 cells (NPC cell line) transfected with pcDNA-NBS1-185Q (8360CC) had significantly higher migration levels than those transfected with pcDNA-NBS1-185E (8360GG) (P = 0.024). These findings suggest that E185Q polymorphism in NBS1 may be a genetic modifier for the occurrence and aggression of NPC.
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The polymorphism and haplotypes of PIN1 gene are associated with the risk of lung cancer in Southern and Eastern Chinese populations.
Hum. Mutat.
PUBLISHED: 03-12-2011
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Peptidyl-prolyl cis/trans isomerase (PPIase), PIN1, has been found to be a critical catalyst that involves in multiple oncogenic signaling pathways. Recently, several putative functional polymorphisms of the PIN1 gene have been identified to be associated with cancer risk. In this study, we tested the hypothesis that two common polymorphisms, c.-842G>C (rs2233678) and c.-667C>T (rs2233679), in the PIN1 promoter are associated with risk of lung cancer. In two independent case-control studies of 1,559 lung cancer cases and 1,679 controls conducted in Southern and Eastern Chinese population, we found that compared with the most common c.-842GG genotype, the carriers of c.-842C variant genotypes (GC + CC) had a decreased risk of lung cancer (odds ratio [OR] = 0.63, 95% confidence interval [CI] = 0.51-0.78, p = 1.13 × 10(-5) ). Although no association was observed between the c.-667C>T polymorphism and cancer risk, we found that the haplotype "C-C" had a greater protective effect (OR = 0.39, 95% CI = 0.23-0.67, p = 5.03 × 10(-4) ). The stratification analysis showed that the protective role of c.-842C variants was more pronounced in current smokers (p = 4.45 × 10(-5) ), especially in male smokers (p = 6.71 × 10(-6) ) and in those who smoked more than 20 pack-years (p = 2.30 × 10(-5) ) and the c.-842C variant genotypes interacted with smoking status (P(interaction) = 0.019) or pack-years smoked (P(interaction) = 0.008) on reducing cancer risk. Further functional assay revealed that the c.-842C variant allele had a lower transcription activity in luciferase assay and a lower DNA-binding ability with nuclear proteins, and low transcription activity in western blot assay. In conclusions, our data suggest that functional c.-842C variants and haplotype "C-C" in the PIN1 promoter contribute to decreased risk of lung cancer by diminishing the promoter activity, which may be susceptibility biomarkers for lung cancer.
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The protective role of polymorphism MKK4-1304 T>G in nasopharyngeal carcinoma is modulated by Epstein-Barr virus infection status.
Int. J. Cancer
PUBLISHED: 02-04-2011
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MKK4 is a candidate tumor suppressor, which acts as a critical mediator of Epstein-Barr Virus (EBV)-induced c-Jun N-terminal kinase (JNK) activation. Functional polymorphism MKK4 -1304T>G has been showed to be protective in colorectal cancer or lung cancer. We hypothesized that genetic variants in the MKK4 promoter were associated with the risk of nasopharyngeal carcinoma (NPC). Two common polymorphisms in MKK4, -1304T>G and -1044A>T were genotyped in two independent case-control panels of Eastern and Southern Chinese populations, totally containing 1237 NPC and 1328 controls. We found that compared to the most common -1304TT genotype, carriers of variant genotypes (-1304TG+GG) were associated with a significantly reduced risk for NPC in total subjects (adjusted OR = 0.78; 95%CI = 0.67-0.94). Further stratification analysis showed that the protective effect was more pronounced in EBV negative status (adjusted OR = 0.51; 95%CI = 0.41-0.68) but restrained in those with EBV infection (adjusted OR = 1.05; 95%CI = 0.88-1.26), and that the -1304GG variant genotypes interacted with EBV negative status on reducing cancer risk (p = 0.011). However, no significant association was observed between the -1044A>T polymorphism and risk of NPC. Our data suggest that the protective role of genetic variant MKK4 -1304T>G is restrained in NPC with EBV infection. These findings implicate the role of EBV and MKK4 -1304 T>G interaction as a causative factor for the NPC.
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Functional polymorphisms in the NBS1 gene and acute lymphoblastic leukemia susceptibility in a Chinese population.
Eur. J. Haematol.
PUBLISHED: 01-25-2011
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As a component of the MRN complex (which is a heterotrimeric protein complex consisting of MRE11, RAD50 and NBS1), NBS1 plays an important role in cellular response to DNA damage and the maintenance of chromosomal integrity. Leukemia is common in NBS1 germ line-mutated patients. The NBS1 E185Q polymorphism (8360G>C, rs1805794) has been frequently studied in some cancers with discordant results, but its association with acute lymphoblastic leukemia (ALL) in Chinese population has not been investigated. Besides, there is no report about the association between NBS1 3UTR variant rs2735383 and ALL risk. In this study, a multiple centre case-control analysis was performed to assess the association between NBS1 polymorphisms and ALL risk. The genotypes and haplotypes were determined in 175 cases and 350 controls, and the associations with risk of ALL were estimated by logistic regression. We observed significant difference in genotype frequencies at the rs1805794 C/G site between cases and controls (P(trend) ?
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Training in contrast detection improves motion perception of sinewave gratings in amblyopia.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 01-01-2011
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PURPOSE. One critical concern about using perceptual learning to treat amblyopia is whether training with one particular stimulus and task generalizes to other stimuli and tasks. In the spatial domain, it has been found that the bandwidth of contrast sensitivity improvement is much broader in amblyopes than in normals. Because previous studies suggested the local motion deficits in amblyopia are explained by the spatial vision deficits, the hypothesis for this study was that training in the spatial domain could benefit motion perception of sinewave gratings. METHODS. Nine adult amblyopes (mean age, 22.1 ± 5.6 years) were trained in a contrast detection task in the amblyopic eye for 10 days. Visual acuity, spatial contrast sensitivity functions, and temporal modulation transfer functions (MTF) for sinewave motion detection and discrimination were measured for each eye before and after training. Eight adult amblyopes (mean age, 22.6 ± 6.7 years) served as control subjects. RESULTS. In the amblyopic eye, training improved (1) contrast sensitivity by 6.6 dB (or 113.8%) across spatial frequencies, with a bandwidth of 4.4 octaves; (2) sensitivity of motion detection and discrimination by 3.2 dB (or 44.5%) and 3.7 dB (or 53.1%) across temporal frequencies, with bandwidths of 3.9 and 3.1 octaves, respectively; (3) visual acuity by 3.2 dB (or 44.5%). The fellow eye also showed a small amount of improvement in contrast sensitivities and no significant change in motion perception. Control subjects who received no training demonstrated no obvious improvement in any measure. CONCLUSIONS. The results demonstrate substantial plasticity in the amblyopic visual system, and provide additional empirical support for perceptual learning as a potential treatment for amblyopia.
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Deficient binocular combination reveals mechanisms of anisometropic amblyopia: signal attenuation and interocular inhibition.
J Vis
PUBLISHED: 01-01-2011
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Amblyopia is a developmental disorder that results in deficits of monocular and binocular vision. It is presently unclear whether these deficits result from attenuation of signals in the amblyopic eye, inhibition by signals in the fellow eye, or both. In this study, we characterize mechanisms underlying anisometropic amblyopia using a binocular phase and contrast combination paradigm and a contrast gain control model. Subjects dichoptically viewed two slightly different images and reported the perceived contrast and phase of the resulting cyclopean percept. We found that the properties of binocular combination were abnormal in many aspects in amblyopic vision. The observed abnormalities can be explained by a combination of (1) attenuated monocular signal in the amblyopic eye, (2) stronger interocular contrast gain control from the fellow eye to the signal in the amblyopic eye (direct interocular inhibition), and (3) stronger interocular contrast gain control from the fellow eye to the contrast gain control signal from the amblyopic eye (indirect interocular inhibition). We conclude that anisometropic amblyopia led to both monocular and interocular deficits. A complete understanding of the mechanisms underlying amblyopia requires studies of both monocular deficits and binocular interactions.
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General and specific perceptual learning in radial speed discrimination.
J Vis
PUBLISHED: 01-01-2011
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The specificity of learning in speed discrimination was examined in three psychophysical experiments. In Experiment 1, half of the observers trained with inward motion direction on a speed discrimination task, whereas the other half trained on the same task but with outward motion direction. The results indicated that significant training-based improvement transferred from a trained radial direction to an untrained radial direction. Experiment 2 confirmed this transfer by showing that complete transfer was obtained even when stimuli moving in an untrained radial direction were used in the transfer task. In Experiment 3, observers were trained at a viewing distance of 114 cm. The results showed that learning transferred partly to the viewing distances of 57 cm and 228 cm. In summary, the present transfer results indicate that reliable generalizations can be obtained in perceptual learning of radial speed discrimination.
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Contrast and phase combination in binocular vision.
PLoS ONE
PUBLISHED: 08-14-2010
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How the visual system combines information from the two eyes to form a unitary binocular representation of the external world is a fundamental question in vision science that has been the focus of many psychophysical and physiological investigations. Ding & Sperling (2006) measured perceived phase of the cyclopean image, and developed a binocular combination model in which each eye exerts gain control on the other eyes signal and over the other eyes gain control. Critically, the relative phase of the monocular sine-waves plays a central role.
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Visual perceptual learning.
Neurobiol Learn Mem
PUBLISHED: 08-12-2010
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Perceptual learning refers to the phenomenon that practice or training in perceptual tasks often substantially improves perceptual performance. Often exhibiting stimulus or task specificities, perceptual learning differs from learning in the cognitive or motor domains. Research on perceptual learning reveals important plasticity in adult perceptual systems, and as well as the limitations in the information processing of the human observer. In this article, we review the behavioral results, mechanisms, physiological basis, computational models, and applications of visual perceptual learning.
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The sexual difference of aging-associated functional degradation in visual cortical cells of rats.
Neurosci. Lett.
PUBLISHED: 07-21-2010
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Function of visual cortical cells declines during normal aging. Whether there are sex-related differences in this functional degradation is still unknown. In the present study we compared the properties of adaptation, onset latency, and signal-to-noise ratio of visual cortical cells between age-matched sexes in order to investigate any sex related difference. Our results show that visual cortical cell function did not differ between young male and young female rats. However, compared with female rats in the same age, the signal-to-noise ratio, but not adaptation or onset latency, was significantly impaired in mid-aged and aged male rats. These results indicate that the functional degradation of visual cortical cells to some extent is associated with sex and therefore, could contribute for the differential degree of cognitive decline that occurs in males and females during senescence.
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A non-synonymous polymorphism Thr115Met in the EpCAM gene is associated with an increased risk of breast cancer in Chinese population.
Breast Cancer Res. Treat.
PUBLISHED: 07-21-2010
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As a tumor-associated antigen and a surface marker of breast cancer stem cells (BCSCs), epithelial cell adhesion molecule (EpCAM) plays an important role in not only cell adhesion, morphogenesis, metastases but also carcinogenesis. A non-synonymous C/T polymorphism (rs1126497) in exon3 of EpCAM causes a transition of 115 amino acid from Met to Thr. Another polymorphism (A/G, rs1421) in the 3UTR causes loss of has-miR-1183 binding. A multiple independent case-control analysis was performed to assess the association between EpCAM genotypes and breast cancer risk. We observed that the variant EpCAM genotype (rs1126497 CT, and TT) was associated with substantially increased risk of breast cancer. Genotyping a total of 1643 individuals with breast cancer and 1818 control subjects in Eastern and Southern Chinese populations showed that rs1126497 CT + TT genotype had an odd ratio of 1.40 (95% confidence interval, 1.16-1.57) for developing breast cancer compared with CC genotype. The allele T increases the risk of breast cancer in a dose-dependent response manner (P (trend) < 0.001). Moreover, compared to breast cancer patients carrying the CC genotype, the EpCAM SNP rs1126497 CT or TT carrier was significantly associated with early breast cancer onset (P = 0.0023). However, no significant difference was found in genotype frequencies at the rs1421 A/G site between cases and controls. These findings suggest that M115T polymorphism in EpCAM may be a genetic modifier for developing breast cancer.
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The role of interleukin-15 polymorphisms in adult acute lymphoblastic leukemia.
PLoS ONE
PUBLISHED: 06-23-2010
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Interleukin-15 (IL-15) plays important roles in the immune system and in the development of hematopoietic cells. Previous studies revealed that five SNPs in IL-15, rs10519612, rs10519613, rs35964658, rs17007695 and rs17015014, were significantly associated with childhood Acute Lymphoblastic Leukemia (ALL) treatment response. In adult ALL, the expression of IL-15 was also correlated with the immunophenotypes of ALL. Therefore, we hypothesize that SNPs of IL-15 might also be associated with adult ALL.
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Association between the Cytotoxic T-lymphocyte antigen 4 +49G > A polymorphism and cancer risk: a meta-analysis.
BMC Cancer
PUBLISHED: 05-05-2010
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As a key gene in the immunosurveillance of cell malignancy, Cytotoxic T-lymphocyte antigen 4 (CTLA-4 is an important negative regulator of T cell activation and proliferation. The CTLA-4 +49G > A polymorphism is one of the most commonly studied polymorphisms in this gene due to its association with cancer risks, but previous results have been conflicting.
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Perceptual learning improves contrast sensitivity of V1 neurons in cats.
Curr. Biol.
PUBLISHED: 03-30-2010
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Perceptual learning has been documented in adult humans over a wide range of tasks. Although the often-observed specificity of learning is generally interpreted as evidence for training-induced plasticity in early cortical areas, physiological evidence for training-induced changes in early visual cortical areas is modest, despite reports of learning-induced changes of cortical activities in fMRI studies. To reveal the physiological bases of perceptual learning, we combined psychophysical measurements with extracellular single-unit recording under anesthetized preparations and examined the effects of training in grating orientation identification on both perceptual and neuronal contrast sensitivity functions of cats.
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Category and perceptual learning in subjects with treated Wilsons disease.
PLoS ONE
PUBLISHED: 02-16-2010
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To explore the relationship between category and perceptual learning, we examined both category and perceptual learning in patients with treated Wilsons disease (WD), whose basal ganglia, known to be important in category learning, were damaged by the disease. We measured their learning rate and accuracy in rule-based and information-integration category learning, and magnitudes of perceptual learning in a wide range of external noise conditions, and compared the results with those of normal controls. The WD subjects exhibited deficits in both forms of category learning and in perceptual learning in high external noise. However, their perceptual learning in low external noise was relatively spared. There was no significant correlation between the two forms of category learning, nor between perceptual learning in low external noise and either form of category learning. Perceptual learning in high external noise was, however, significantly correlated with information-integration but not with rule-based category learning. The results suggest that there may be a strong link between information-integration category learning and perceptual learning in high external noise. Damage to brain structures that are important for information-integration category learning may lead to poor perceptual learning in high external noise, yet spare perceptual learning in low external noise. Perceptual learning in high and low external noise conditions may involve separate neural substrates.
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An insertion/deletion polymorphism at miRNA-122-binding site in the interleukin-1alpha 3 untranslated region confers risk for hepatocellular carcinoma.
Carcinogenesis
PUBLISHED: 11-16-2009
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Hepatocellular carcinoma (HCC) is the fifth most common malignancy caused by environmental and genetic factors. MicroRNAs (miRNAs) are a class of short non-coding RNAs with posttranscriptional regulatory functions. They participate in diverse biological pathways and function as gene regulators. Genetic polymorphisms in 3 untranslated regions (3 UTRs) targeted by miRNAs alter the strength of miRNA binding, with consequences on regulation of target genes thereby affecting the individuals cancer risk. We have previously predicted polymorphisms falling in miRNA-binding regions of cancer genes. We selected an insertion/deletion (Indel) polymorphism (rs3783553) in the 3 UTR of interleukin (IL)-1alpha (IL1A) for a case-control study in a Chinese population. With samples from 403 HCC patients and 434 healthy control individuals, strong evidence of association was observed for the variant homozygote. This association was validated in a second independent case-control study with 1074 HCC patients and 1239 healthy control individuals (odds ratio = 0.62; 95% confidence interval = 0.49-0.78). We further show that the TTCA insertion allele for rs3783553 disrupts a binding site for miR-122 and miR-378, thereby increasing transcription of IL-1alpha in vitro and in vivo. These findings suggest that functional polymorphism rs3783553 in IL1A could contribute to HCC susceptibility. Considering IL-1alpha affects not only various phases of the malignant process, such as carcinogenesis, tumor growth and invasiveness, but also patterns of interactions between malignant cells and the hosts immune system, our results indicated that IL-1alpha may be a promising target for immunotherapy, early diagnosis and intervention of HCC.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.