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Successful myelination of the peripheral nervous system depends upon induction of major protein components of myelin, such as peripheral myelin protein 22 (PMP22). Myelin stability is also sensitive to levels of PMP22, as a 1.4 Mb duplication on human chromosome 17, resulting in three copies ofPMP22, is the most common cause of the peripheral neuropathy Charcot-Marie-Tooth disease. The transcription factor Egr2/Krox20 is required for induction of high level expression of Pmp22 in Schwann cells but its activation elements have not yet been determined. Using chromatin immunoprecipitation analysis of the ratPmp22locus, we found a major peak of Egr2 binding within the large intron of thePmp22gene. Analysis of a 250 bp region within the largest intron showed that it is strongly activated by Egr2 expression in reporter assays. Moreover, this region contains conserved binding sites not only for Egr2 but also for Sox10, which is also required for Schwann cell development. Our analysis shows that Sox10 is required for optimal activity of the intronic site as well asPMP22expression. Finally, mouse transgenic analysis revealed tissue-specific expression of this intronic sequence in peripheral nerve. Overall, these data show that Egr2 and Sox10 activity are directly involved in mediating the developmental induction ofPmp22expression.

Ga-doped ZnO (GZO) nanowires have been synthesized by thermal evaporation with gallium metal as the dopant source. The morphology, microstructure and chemical composition were determined by field emission scanning electron microscopy (FE-SEM), X-ray diffraction, high-resolution transmission electron microscopy (HRTEM), electron paramagnetic resonance (EPR), and X-ray photoelectron spectroscopy (XPS). The investigation confirmed that the GZO nanowires were the wurtzite hexagonal structures. These doped nanowires have diameters in the range 30–70 nm and lengths of several hundreds of nanometers with growth direction along the (1 0 0) crystal plane. The optical properties from the cathodoluminescence (CL) and photoluminescence (PL) spectrum show that GZO nanowires exhibit a relative weak ultraviolet emission (UV) and a strong green emission. The UV emission for ZnO and GZO nanowires is attributed to near band-edge emission from recombination of free excitons. Furthermore, the green emission is attributed to oxygen vacancy and gallium impurity energy levels. Field emission measurements demonstrate that the GZO possesses good performance with a turn-on field of 3.4 V/μm at a current density of 10 μA/cm 2 , a threshold field of 5.4 V/μm at a current density of 1 mA/cm 2 , and a field-enhancement factor β of 5945. These results are very helpful for the design, fabrication and optimization of integrated optoelectronic nanodevices using GZO nanowires.

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression and have been implicated in the pathogenesis of cancer. In this study, we applied next generation sequencing techniques to comprehensively assess miRNA expression, identify genetic variants of miRNA genes, and screen for alterations in miRNA binding sites in a patient with acute myeloid leukemia. RNA sequencing of leukemic myeloblasts or CD34+ cells pooled from healthy donors showed that 472 miRNAs were expressed, including 7 novel miRNAs, some of which displayed differential expression. Sequencing of all known miRNA genes revealed several novel germline polymorphisms but no acquired mutations in the leukemia genome. Analysis of the sequence of the 3′-untranslated regions (UTRs) of all coding genes identified a single somatic mutation in the 3′-UTR of TNFAIP2, a known target of the PML-RARα oncogene. This mutation resulted in translational repression of a reporter gene in a Dicer-dependent fashion. This study represents the first complete characterization of the “miRNAome” in a primary human cancer and suggests that generation of miRNA binding sites in the UTR regions of genes is another potential mechanism by which somatic mutations can affect gene expression.

Myelination of peripheral nerves by Schwann cells depends upon a gene regulatory network controlled by early growth response Egr2/Krox20, which is specifically required for Schwann cells to initiate and maintain myelination. To elucidate the mechanism by which Egr2 regulates gene expression during myelination, we have performed chromatin immunoprecipitation analysis on myelinating rat sciatic nerve in vivo. The resulting samples were applied to a tiled microarray consisting of a broad spectrum of genes that are activated or repressed in Egr2-deficient mice. The results show extensive binding within myelin-associated genes, as well as some genes that become repressed in myelinating Schwann cells. Many of the Egr2 peaks coincide with regions of open chromatin, which is a marker of enhancer regions. In addition, further analysis showed that there is substantial colocalization of Egr2 binding with Sox10, a transcription factor required for Schwann cell specification and other stages of Schwann cell development. Finally, we have found that Egr2 binds to promoters of several lipid biosynthetic genes, which is consistent with their dramatic up-regulation during the formation of lipid-rich myelin. Overall, this analysis provides a locus-wide profile of Egr2 binding patterns in major myelin-associated genes using myelinating peripheral nerve.

In this study, we have synthesized N-doped s-Ga 2 O 3 nanowires on a p-type Si (100) substrate at the temperature of 850 °C through evaporation to modulate the spectra of the luminescence emission. Both TEM and XRD analyses confirmed that N-doped s-Ga 2 O 3 is monoclinic with a uniform mean diameter of 30 nm and a length up to several tens of micrometers. As determined by selected area diffraction (SAD), the growth direction of N-doped s-Ga 2 O 3 nanowires is [002]. The optical properties of the N-doped s-Ga 2 O 3 nanowires were studied by cathodoluminescence (CL) at the 10 and 300 K, exhibiting a UV and red light emission as a function of the nitrogen dopant. The results serve to reinforce the potential of N-doped s-Ga 2 O 3 nanowires for optoelectronic device applications.

Acute promyelocytic leukemia (APL) is characterized by the t(15;17) chromosomal translocation, which results in fusion of the retinoic acid receptor alpha (RARA) gene to another gene, most commonly promyelocytic leukemia (PML). The resulting fusion protein, PML-RARA, initiates APL, which is a subtype (M3) of acute myeloid leukemia (AML). In this report, we identify a gene expression signature that is specific to M3 samples; it was not found in other AML subtypes and did not simply represent the normal gene expression pattern of primary promyelocytes. To validate this signature for a large number of genes, we tested a recently developed high throughput digital technology (NanoString nCounter). Nearly all of the genes tested demonstrated highly significant concordance with our microarray data (P < 0.05). The validated gene signature reliably identified M3 samples in 2 other AML datasets, and the validated genes were substantially enriched in our mouse model of APL, but not in a cell line that inducibly expressed PML-RARA. These results demonstrate that nCounter is a highly reproducible, customizable system for mRNA quantification using limited amounts of clinical material, which provides a valuable tool for biomarker measurement in low-abundance patient samples.

Summary Objective To provide a more complete picture of the effect of interleukin-1 beta (IL-1β) on adult human articular chondrocyte gene expression, in contrast to the candidate gene approach. Design Chondrocytes from human knee cartilage were cultured in medium containing IL-1β. Changes in gene expression were analyzed by microarray and reverse transcriptase-polymerase chain reaction analysis. The ability of transforming growth factor beta-1 (TGF-β1), fibroblast growth factor (FGF)-18, and bone morphogenetic protein 2 (BMP-2) to alter the effects of IL-1β was analyzed. Computational analysis of the promoter regions of differentially expressed genes for transcription factor binding motifs was performed. Results IL-1β-treated human chondrocytes showed significant increases in the expression of granulocyte colony stimulating factor-3, endothelial leukocyte adhesion molecule 1 and leukemia inhibitory factor as well as for a large group of chemokines that include CXCL1, CXCL2, CXCL3, CXCL5, CXCL6, CXCL8, CCL2, CCL3, CCL4, CCL5, CCL8, CCL20, CCL3L1, CX3CL1 and the cytokine IL-6. As expected, the mRNA for matrix metalloproteinase (MMP)-13 and BMP-2 also increased while mRNA for the matrix genes COL2A1 and aggrecan was down-regulated. A subset of chemokines increased rapidly at very low levels of IL-1β. The phenotype induced by IL-1β was partially reversed by TGF-β1, but not by BMP-2. In the presence of IL-1β, FGF-18 increased expression of ADAMTS-4, aggrecan, BMP-2, COL2A1, CCL3, CCL4, CCL20, CXCL1, CXCL3, CXCL6, IL-1β, IL-6, and IL-8 and decreased ADAMTS-5, MMP-13, CCL2, and CCL8. Computational analysis revealed a high likelihood that the most up-regulated chemokines are regulated by the transcription factors myocyte enhancer binding factor-3 (MEF-3), CCAAT/enhancer binding protein (C/EBP) and nuclear factor-kappa B (NF-κB). Conclusion IL-1β has a diverse effect on gene expression profile in human chondrocytes affecting matrix genes as well as chemokines and cytokines. TGF-β1 has the ability to antagonize some of the phenotype induced by IL-1β.

The myelin sheath insulates axons and allows for rapid salutatory conduction in the nervous system of all vertebrates. The formation of peripheral myelin requires expression of the transcription factor Egr2, which is responsible for inducing such essential myelin-associated genes asMpz,Mbp,Pmp22, andMag. Using microarray analysis to compare gene expression patterns in peripheral nerve during development, during remyelination after nerve injury, and in a congenital hypomyelinating mouse model, we identified an evolutionarily conserved novel component of myelin called Mp11 (myelin protein of 11 kDa). The Mp11 genomic locus contains multiple conserved Egr binding sites, and Mp11 induction is regulated by the expression of Egr2. Similar to other Egr2-dependent genes, it is induced during developmental myelination and remyelination after nerve injury. Mp11 is a glycoprotein expressed preferentially in the myelin of the peripheral nervous system versus CNS and is specifically localized to the Schmidt-Lanterman incisures and paranodes of peripheral nerve. The Mp11 protein contains no identifiable similarity to other known protein domains or motifs. However, like other myelin genes, strict Mp11 expression levels are a requirement for thein vitromyelination of DRG neurons, indicating that this previously uncharacterized gene product is a critical component of peripheral nervous system myelin.

Proneural basic helix–loop–helix proteins are key regulators of neurogenesis but their ‘proneural’ function is not well understood, partly because primary targets have not been systematically defined. Here, we identified direct transcriptional targets of the bHLH proteins Neurogenin and NeuroD and found that primary roles of these transcription factors are to induce regulators of transcription, signal transduction, and cytoskeletal rearrangement for neuronal differentiation and migration. We determined targets induced in both Xenopus and mouse, which represent evolutionarily conserved core mediators of Neurogenin and NeuroD activities. We defined consensus sequences for Neurogenin and NeuroD binding and identified responsive enhancers in seven shared target genes. These enhancers commonly contained clustered, conserved consensus‐binding sites and drove neural‐restricted transgene expression in Xenopus embryos. We then used this enhancer signature in a genome‐wide computational approach to predict additional Neurogenin/NeuroD target genes involved in neurogenesis. Taken together, these data demonstrate that Neurogenin and NeuroD preferentially recognize neurogenesis‐related targets through an enhancer signature of clustered consensus‐binding sites and regulate neurogenesis by activating a core set of transcription factors, which build a robust network controlling neurogenesis.

Myelination in the PNS is accompanied by a large induction of the myelin protein zero (Mpz) gene to produce the most abundant component in peripheral myelin. Analyses of knockout mice have shown that the EGR2/Krox20 and SOX10 transcription factors are required for Mpz expression. Our recent work has shown that the dominant EGR2 mutations associated with human peripheral neuropathies cause disruption of EGR2/SOX10 synergy at specific sites, including a conserved enhancer element in the first intron of the Mpz gene. Further investigation of Egr2/Sox10 interactions reveals that activation of the Mpz intron element by Egr2 requires both Sox10-binding sites. In addition, both Egr1 and Egr3 cooperate with Sox10 to activate this element, which indicates that this capacity is conserved among Egr family members. Finally, a conserved composite structure of Egr2/Sox10-binding sites in the genes encoding Mpz, myelin-associated glycoprotein and myelin basic protein genes was used to screen for similar modules in other myelin genes, revealing a potential regulatory element in the periaxin gene. Overall, these results elucidate a working model for developmental regulation of Mpz expression, several facets of which extend to regulation of other peripheral myelin genes.

All four mammalian Notch proteins interact with a single DNA-binding protein (RBP-jkappa), yet they are not equivalent in activating target genes. Parallel assays of three Notch-responsive promoters in several cell lines revealed that relative activation strength is dependent on protein module and promoter context more than the cellular context. Each Notch protein reads binding site orientation and distribution on the promoter differently; Notch1 performs extremely well on paired sites, and Notch3 prefers single sites in conjunction with a proximal zinc finger transcription factor. Although head-head sites can elicit a Notch response on their own, use of CBS (CSL binding site) in tail-tail orientation is context-dependent. Bias for specific DNA elements is achieved by interplay between the N-terminal RAM (RBP-jkappa-associated molecule/ankyrin region), which interprets CBS proximity and orientation, and the C-terminal transactivation domain that interacts specifically with the transcription machinery or nearby factors. To confirm the prediction that modular design underscores the evolution of functional divergence between Notch proteins, we generated a synthetic Notch protein (Notch1 ankyrin with Notch3 transactivation domain) that displayed superior signaling strength on the hes5 promoter. Consistent with the prediction that "preferred" targets (Hes1) should respond faster and at lower Notch concentration than other targets, we showed that Hes5-GFP was extinguished fast and recovered slowly, whereas Hes1-GFP was inhibited late and recovered quickly after a pulse of DAPT in metanephroi cultures.

An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying transcription regulation, i.e., (1) the identification of common transcriptional regulators of a set of coexpressed genes; (2) the identification of genes that are regulated by one or several transcription factors. In this study, a systematic and statistical approach was taken to accomplish these tasks by establishing an integrated model considering all of the promoters and characterized transcription factors (TFs) in the genome. A promoter analysis pipeline (PAP) was developed to implement this approach. PAP was tested using coregulated gene clusters collected from the literature. In most test cases, PAP identified the transcription regulators of the input genes accurately. When compared with chromatin immunoprecipitation experiment data, PAP's predictions are consistent with the experimental observations. When PAP was used to analyze one published expression-profiling data set and two novel coregulated gene sets, PAP was able to generate biologically meaningful hypotheses. Therefore, by taking a systematic approach of considering all promoters and characterized TFs in our model, we were able to make more reliable predictions about the regulation of gene expression in mammalian organisms.

Androgen signaling via the androgen receptor (AR) transcription factor is crucial to normal prostate homeostasis and prostate tumorigenesis. Current models of AR function are predominantly based on studies of prostate-specific antigen regulation in androgen-responsive cell lines. To expand on these in vitro paradigms, we used the mouse prostate to elucidate the mechanisms through which AR regulates another direct target, FKBP5, in vivo. FKBP5 encodes an immunophilin that has been previously implicated in glucocorticoid and progestin signaling pathways and that likely influences prostate physiology in the presence of androgens. In this work, we show that androgens directly regulate FKBP5 via an interaction between the AR and a distal enhancer located 65 kb downstream of the transcription start site in the fifth intron of the FKBP5 gene. We have found that AR selectively recruits cAMP response element-binding protein to this enhancer. These interactions, in turn, result in chromatin remodeling that affects the enhancer proper but not the FKBP5 locus as a whole. Furthermore, in contrast to prostate-specific antigen-regulatory mechanisms, we show that transactivation of the FKBP5 gene does not rely on a single looping complex to mediate communication between the distal enhancer and proximal promoter. Rather, the distal enhancer complex and basal transcription apparatus communicate indirectly with one another, implicating a regulatory mechanism that has not been previously appreciated for AR target genes.

Multi-walled carbon nanotubes (MWCNTs) synthesized by thermal chemical vapor deposition have been successfully purified by using efficient microwave digestion method. Recently, various purification methods have been provided to eliminate metal catalysts and most were acid treatment procedures that take long time and damage the structure of nanotubes. Comparing to these methods, microwave digestion takes a tremendous advantage because the acid in this approach can absorb microwave energy rapidly and dissolve metal efficiently without damaging the wall structure and the processing time could be the shortest. The ability of microwave digestion method was studied by various experimental parameters. The efficient purification proceeded for 90 min and at 210 °C with 5 M nitric acid treatment in the microwave digestion system to dissolve the metal catalyst. High-resolution transition electron microscopy and Raman spectra were used to characterize the specimen. Purities were characterized by thermogravimetric analysis (TGA). Results showed that the amount of catalyst decreased with increasing acid treatment time and concentration. Purity of MWCNTs achieved as high as about 99.9%. This study presents a highly efficient purification method for carbon nanotubes with high purity and no structure destruction. In addition, carbon nanotubes synthesized by various methods were also purified and the results were comprehensively discussed.

In this study, optical properties of the nitrogen-doped β -Ga 2 O 3 nanowires (N-doped β -Ga 2 O 3 NWs) were synthesized by exposing β -Ga 2 O 3 NWs under high input power nitrogen plasma (2 kW), using a microwave plasma enhanced chemical vapor deposition (MPECVD) system. The nitrogen contents in the NWs were as-prepared about 7.4, 8.9, 9.7, 13.9, 19.3, and 26.6 at.%, respectively. Low temperature (10 K) cathodoluminescence (CL) spectra exhibit significantly different optical properties for the different nitrogen contents. The CL result of the N-doped β -Ga 2 O 3 NWs (210 s N 2 plasma treatment) exhibited four distinct emission peaks at 378, 516, 759, and 970 nm. The possible light emission mechanism including the effect of the nitrogen dopant was discussed.

A major goal of cancer genome sequencing is to identify mutations or other somatic alterations that can be targeted by selective and specific drugs. dGene is an annotation tool designed to rapidly identify genes belonging to one of ten druggable classes that are frequently targeted in cancer drug development. These classes were comprehensively populated by combining and manually curating data from multiple specialized and general databases. dGene was used by The Cancer Genome Atlas squamous cell lung cancer project, and here we further demonstrate its utility using recently released breast cancer genome sequencing data. dGene is designed to be usable by any cancer researcher without the need for support from a bioinformatics specialist. A full description of dGene and options for its implementation are provided here.

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profile 178 lung squamous cell carcinomas to provide a comprehensive landscape of genomic and epigenomic alterations. We show that the tumour type is characterized by complex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 segments of copy number alteration per tumour. We find statistically recurrent mutations in 11 genes, including mutation of TP53 in nearly all specimens. Previously unreported loss-of-function mutations are seen in the HLA-A class I major histocompatibility gene. Significantly altered pathways included NFE2L2 and KEAP1 in 34%, squamous differentiation genes in 44%, phosphatidylinositol-3-OH kinase pathway genes in 47%, and CDKN2A and RB1 in 72% of tumours. We identified a potential therapeutic target in most tumours, offering new avenues of investigation for the treatment of squamous cell lung cancers., National Institutes of Health (U.S.) (Grant U24 CA126561), National Institutes of Health (U.S.) (Grant U24 CA126551), National Institutes of Health (U.S.) (Grant U24 CA126554), National Institutes of Health (U.S.) (Grant U24 CA126543), National Institutes of Health (U.S.) (Grant U24 CA126546), National Institutes of Health (U.S.) (Grant U24 CA126563), National Institutes of Health (U.S.) (Grant U24 CA126544), National Institutes of Health (U.S.) (Grant U24 CA143845), National Institutes of Health (U.S.) (Grant U24 CA143858), National Institutes of Health (U.S.) (Grant U24 CA144025), National Institutes of Health (U.S.) (Grant U24 CA143882), National Institutes of Health (U.S.) (Grant U24 CA143866), National Institutes of Health (U.S.) (Grant U24 CA143867), National Institutes of Health (U.S.) (Grant U24 CA143848), National Institutes of Health (U.S.) (Grant U24 CA143840), National Institutes of Health (U.S.) (Grant U24 CA143835), National Institutes of Health (U.S.) (Grant U24 CA143799), National Institutes of Health (U.S.) (Grant U24 CA143883), National Institutes of Health (U.S.) (Grant U24 CA143843), National Institutes of Health (U.S.) (Grant U54 HG003067), National Institutes of Health (U.S.) (Grant U54 HG003079), National Institutes of Health (U.S.) (Grant U54 HG003273)

The formation and characterization of one-dimensional nanomaterials have attracted considerable attention because of their unique physical and chemical properties [1–6]. For example, they can be applied in organic light-emitting diodes (OLEDs), solid lubricants, DNA analysis, and electrochromic devices [7–10]. Because of their semiconducting properties and high surface areas, transition metal oxide nanostructures have been used in a variety of research projects that developed device-oriented nanostructures. For example, tungsten oxide nanostructures such as nanowires, nanorods, nanotubes, nanobelts, and nanofibers have well-known electrical, mechanical, gasochromic, and photoelectrochromic properties that make them very useful for various applications, including field-emission devices, electrochromic devices, light-emitting diodes, and gas and chemical sensors [11–15]. Recently, nanostructured tungsten oxide materials have been of great scientific and applied interest.

A large set of chemokines is highly up-regulated in human chondrocytes in response to IL-1β (Sandell, L. J., Xing, X., Franz, C., Davies, S., Chang, L. W., and Patra, D. (2008) Osteoarthr. Cartil. 16, 1560–1571). To investigate the mechanism of transcriptional regulation, deletion constructs of selected chemokine gene promoters, the human CCL3 (MIP-1α) and CCL4 (MIP-1β), were transfected into human chondrocytes with or without IL-1β. The results show that an IL-1β-responsive element is located between bp −300 and −140 of the CCL3 promoter and between bp −222 and −100 of the CCL4 promoter. Because both of these elements contain CCAAT/enhancer-binding protein β (C/EBPβ) motifs, the function of C/EBPβ was examined. IL-1β stimulated the expression of C/EBPβ, and the direct binding of C/EBPβ to the C/EBPβ motif was confirmed by EMSA and ChIP analyses. The −300 bp CCL3 promoter and −222 bp CCL4 promoter were strongly up-regulated by co-transfection with the C/EBPβ expression vector. Mutation of the C/EBPβ motif and reduction of C/EBPβ expression by siRNA decreased the up-regulation. Additionally, another cytokine-related transcription factor, NF-κB, was also shown to be involved in the up-regulation of chemokines in response to IL-1β, and the binding site was identified. The regulation of C/EBPβ and NF-κB was confirmed by the inhibition by C/EBPβ and NF-κB and by transfection with C/EBPβ and NF-κB expression vectors in the presence or absence of IL-1β. Taken together, our results suggest that C/EBPβ and NF-κB are both involved in the IL-1β-responsive up-regulation of chemokine genes in human chondrocytes. Time course experiments indicated that C/EBPβ gradually and steadily induces chemokine up-regulation, whereas NF-κB activity was highest at the early stage of chemokine up-regulation.

To elucidate the effects of resistin on human articular chondrocytes and to generate a picture of their regulation at the transcriptional and posttranscriptional levels.Human articular chondrocytes were cultured with resistin. Changes in gene expression were analyzed at various doses and times. Cells were also treated with the transcription inhibitor actinomycin D after resistin treatment or with the NF-kappaB inhibitor IKK-NBD before resistin treatment. Gene expression was tested by quantitative real-time polymerase chain reaction. Computational analysis for transcription factor binding motifs was performed on the promoter regions of differentially expressed genes. TC-28 chondrocytes were transfected with CCL3 and CCL4 promoter constructs, pNF-kappaB reporter, and NF-kappaB and CCAAT/enhancer binding protein beta (C/EBPbeta) expression vectors with or without resistin.Resistin-treated human articular chondrocytes increased the expression of cytokines and chemokines. Levels of messenger RNA (mRNA) for matrix metalloproteinase 1 (MMP-1), MMP-13, and ADAMTS-4 also increased, while type II collagen alpha1 (COL2A1) and aggrecan were down-regulated. The cytokine and chemokine genes could be categorized into 3 groups according to the pattern of mRNA expression over a 24-hour time course. One pattern suggested rapid regulation by mRNA stability. The second and third patterns were consistent with transcriptional regulation. Computational analysis suggested the transcription factors NF-kappaB and C/EBPbeta were involved in the resistin-induced up-regulation. This prediction was confirmed by the cotransfection of NF-kappaB and C/EBPbeta and the IKK-NBD inhibition.Resistin has diverse effects on gene expression in human chondrocytes, affecting chemokines, cytokines, and matrix genes. Messenger RNA stabilization and transcriptional up-regulation are involved in resistin-induced gene expression in human chondrocytes.

In this paper, we proposed a backoff mechanism to improve the performance of initial ranging for the IEEE 802.16 standard. In the proposed scheme, the size of contention window in the initial ranging is combined with exponential and linear backoff mechanisms, and it is adjusted based on the current network environments. In addition, a threshold in the proposed scheme is set to find out the current network situation. If the contention window size is smaller than the threshold, the contention window size is tuned exponentially in response to a light network traffic load. On the other hand, when the contention window size is larger than the threshold, the contention window size is tuned linearly in response to a congested scenario. The numerical simulation results show that the proposed scheme can achieve a better performance in terms of collision rate, average access delay, and system throughput in both light and congested environments.

Multi-camera systems have been widely used in many video surveillance applications. When an event happens and is monitored across multiple cameras, it is easy for an expert to generate the corresponding spatial representation to comprehend the series of event. However, it is not trivial for users new to the environment. With support from psychological evidences, we propose an approach to mimic generating pictorial-based representation of mental images when a target is moving across the views of cameras. First we conduct a ball-rolling experiment to compare this approach with others. The empirical results demonstrate that the performance of users with this approach is significantly better than others. We suggest that it is because this approach is better for users to preserve spatial representation of the environment while transiting views between cameras. Then we propose a framework to realize this approach. The demonstrations in different situations indicate the validity of such framework.

Ga-doped ZnO nanowire has a wurtzite hexagonal structure and has been prepared in a horizontal tube furnace by thermal chemical vapor deposition method . In this work, we fabricate the Ga-doped ZnO nanowires without a metalized catalyst through the thermal evaporation of the Zn powers and Ga metals at a low growth temperature of 550degC .Temperature is the critical experimental parameter for the formation of Ga-doped ZnO nanowires.This evaporation process can be attributed to the Ga dopant in the lattice position of he ZnO nanowires. As shown in scanning electron microscopy (SEM), nanowires of different diameters are evenly arranged on the Si substrate and nucleated via a self-catalysed mechanism by depositing a layer of ZnO film as the crystallization plant before growing ZnO nanowires on the film. Self-catalyzed growth of Ga-doped ZnO nanowires are of diameters 35-150 nm and lengths up to several ones of micrometers. High resolution Transmission electron microscope (HRTEM) lattice image of Ga doped ZnO nanowires, wherein those nanowires are seen a lattice of a=3.25 Aring and c=5.19 Aring. As determine by selected area diffraction (SAD), the growth direction of Ga-doped ZnO nanowires is [001] and the nanowire consists of single-crystalline ZnO crystals.The luminescence spectra of the Ga-doped ZnO nanowires exhibit a UV band at 374 nm and a strong green band at 498 nm. In addition, the Ga-doped ZnO nanowires with different diameters have a larger green light/UV ratio due to the recombination of holes with the electrons occupying the singly ionized more O vacancies that are larger in number. By virue of the doping of Ga, we observe that Ga-doped ZnO nanowires becomes broader and shifts to a longer wavelength 498 nm at a lower energy and a strong green emission as compared to the undoped one in the cathodoluminescence and photoluminescence spectra. The Ga-doped ZnO nanowires have a greater field-enhancement factor than the undoped ZnO nanowires. The Ga-doped ZnO nanowires with a low turn on field (12 Vmum-1) are apparently lower than the undoped ZnO nanowires. Our results demonstrate that Ga-doped ZnO nanowires can provide the possibility of application in optoelectric nanodevices.

Chondrocyte gene regulation is important for the generation and maintenance of cartilage tissues. Several regulatory factors have been identified that play a role in chondrogenesis, including the positive transacting factors of the SOX family such as SOX9, SOX5, and SOX6, as well as negative transacting factors such as C/EBP and delta EF1. However, a complete understanding of the intricate regulatory network that governs the tissue-specific expression of cartilage genes is not yet available. We have taken a computational approach to identify cis-regulatory, transcription factor (TF) binding motifs in a set of cartilage characteristic genes to better define the transcriptional regulatory networks that regulate chondrogenesis. Our computational methods have identified several TFs, whose binding profiles are available in the TRANSFAC database, as important to chondrogenesis. In addition, a cartilage-specific SOX-binding profile was constructed and used to identify both known, and novel, functional paired SOX-binding motifs in chondrocyte genes. Using DNA pattern-recognition algorithms, we have also identified cis-regulatory elements for unknown TFs. We have validated our computational predictions through mutational analyses in cell transfection experiments. One novel regulatory motif, N1, found at high frequency in the COL2A1 promoter, was found to bind to chondrocyte nuclear proteins. Mutational analyses suggest that this motif binds a repressive factor that regulates basal levels of the COL2A1 promoter.

Objective: To explore the role of endothelin-1 (ET-1) on lipid metabolism, we examined the effect of ET-1 on lipolysis in rat adipocytes. Research Methods and Procedure: Adipocytes isolated from male Sprague-Dawley rats, weighing 400 to 450 grams, were incubated in Krebs-Ringer buffer with or without 10−7 M ET-1 for various times or with various concentrations of ET-1 for 4 hours; then glycerol release into the incubation medium was measured. In addition, selective ETAR and ETBR blockers were used to identify the ET receptor subtype involved. We also explored the involvement of cyclic adenosine monophosphate (cAMP) in ET-1-stimulated lipolysis using an adenylyl cyclase inhibitor and by measuring changes in intracellular cAMP levels in response to ET-1 treatment. To further explore the underlying mechanism of ET-1 action, we examined the involvement of the extracellular signal-regulated kinase (ERK)-mediated pathways. Results: Our results showed that ET-1 caused lipolysis in rat adipocytes in a time- and dose-dependent manner. BQ610, a selective ETAR blocker, blocked this effect. The adenylyl cyclase inhibitor, 2′, 5′-dideoxyadenosine, had no effect on ET-1-stimulated lipolysis. ET-1 did not induce an increase in intracellular cAMP levels. In addition, ET-1-induced lipolysis was blocked by inhibition of ERK activation using PD98059. Coincubation of cells with ET-1 and insulin suppressed ET-1-stimulated lipolysis. Discussion: These findings show that ET-1 stimulates lipolysis in rat adipocytes through the ETAR and activation of the ERK pathway. The underlying mechanism is cAMP-independent. However, this non-conventional lipolytic effect of ET-1 is inhibited by the anti-lipolytic effect of insulin.

All four mammalian Notch proteins interact with a single DNA-binding protein (RBP-jkappa), yet they are not equivalent in activating target genes. Parallel assays of three Notch-responsive promoters in several cell lines revealed that relative activation strength is dependent on protein module and promoter context more than the cellular context. Each Notch protein reads binding site orientation and distribution on the promoter differently; Notch1 performs extremely well on paired sites, and Notch3 prefers single sites in conjunction with a proximal zinc finger transcription factor. Although head-head sites can elicit a Notch response on their own, use of CBS (CSL binding site) in tail-tail orientation is context-dependent. Bias for specific DNA elements is achieved by interplay between the N-terminal RAM (RBP-jkappa-associated molecule/ankyrin region), which interprets CBS proximity and orientation, and the C-terminal transactivation domain that interacts specifically with the transcription machinery or nearby factors. To confirm the prediction that modular design underscores the evolution of functional divergence between Notch proteins, we generated a synthetic Notch protein (Notch1 ankyrin with Notch3 transactivation domain) that displayed superior signaling strength on the hes5 promoter. Consistent with the prediction that "preferred" targets (Hes1) should respond faster and at lower Notch concentration than other targets, we showed that Hes5-GFP was extinguished fast and recovered slowly, whereas Hes1-GFP was inhibited late and recovered quickly after a pulse of DAPT in metanephroi cultures.

The study of transcriptional regulation at the genomic level has been hindered by the lack of functional annotation in the putative regulatory regions. Phylogenetic footprinting, in which cross-species sequence alignment among orthologous genes is applied to locate conserved sequence blocks, is an effective strategy to attack this problem. Single nucleotide polymorphisms (SNPs) in transcription factor (TF) binding sites contribute to the heterogeneity of TF binding sites and might disrupt or enhance their regulatory activity. The correlation of SNPs with the TF sites will not only help in functional evaluation of SNPs, but will also help in the study of transcription regulation by focusing attention on specific TF sites. PromoLign (http://polly.wustl.edu/promolign/main.html) is an online database application that presents SNPs and TF binding profiles in the context of human-mouse orthologous sequence alignment with a hyperlinked graphical interface. PromoLign could be applied to a variety of SNPs and transcription related studies, including association genetics, population genetics, and pharmacogenetics. Hum Mutat 23:534–539, 2004. © 2004 Wiley-Liss, Inc.

There is compelling in vivo evidence from reports on human genetic mutations and transgenic mice that some microRNAs (miRNAs) play an important functional role in regulating skeletal development and growth. A number of published in vitro studies also point toward a role for miRNAs in controlling chondrocyte gene expression and differentiation. However, information on miRNAs that may regulate a specific phase of chondrocyte differentiation (i.e. production of progenitor, differentiated or hypertrophic chondrocytes) is lacking. To attempt to bridge this knowledge gap, we have investigated miRNA expression patterns in human embryonic cartilage tissue. Specifically, a developmental time point was selected, prior to endochondral ossification in the embryonic limb, to permit analysis of three distinct populations of chondrocytes. The location of chondroprogenitor cells, differentiated chondrocytes and hypertrophic chondrocytes in gestational day 54–56 human embryonic limb tissue sections was confirmed both histologically and by specific collagen expression patterns. Laser capture microdissection was utilized to separate the three chondrocyte populations and a miRNA profiling study was carried out using TaqMan® OpenArray® Human MicroRNA Panels (Applied Biosystems®). Here we report on abundantly expressed miRNAs in human embryonic cartilage tissue and, more importantly, we have identified miRNAs that are significantly differentially expressed between precursor, differentiated and hypertrophic chondrocytes by 2-fold or more. Some of the miRNAs identified in this study have been described in other aspects of cartilage or bone biology, while others have not yet been reported in chondrocytes. Finally, a bioinformatics approach was applied to begin to decipher developmental cellular pathways that may be regulated by groups of differentially expressed miRNAs during distinct stages of chondrogenesis. Data obtained from this work will serve as an important resource of information for the field of cartilage biology and will enhance our understanding of miRNA-driven mechanisms regulating cartilage and endochondral bone development, regeneration and repair.

Abstract 524 Understanding epigenetic mechanisms of gene regulation will provide an unprecedented opportunity for therapeutic intervention in cancer because, unlike genetic lesions, pathogenic changes to the epigenome are reversible. Non-Hodgkin Lymphoma (NHL), which strikes 70,000 Americans annually, is characterized by deregulated expression of large gene cohorts that mediate unchecked cell growth, the molecular basis of which remains poorly understood. Recently, recurrent somatic mutations were identified in chromatin modifier genes (EZH2, MLL2, EP300) in ∼30% of NHL, suggesting that epigenetic dysregulation may be a common mechanism for widespread gene expression changes. Indeed, previous studies have demonstrated evidence of aberrant DNA methylation in lymphoma. Moreover, NHL-specific regulatory elements are attractive candidates for therapeutic targeting, because reversal of their aberrant epigenetic profile would restore normal gene expression, while leaving normal cells intact. In this study, we performed integrative epigenomic, genomic, and transcriptomic profiling of purified CD19+ B cells from excisional lymph node biopsies and peripheral blood (PB, when available and free of circulating lymphoma) in 84 patients with NHL (Diffuse Large B cell lymphoma (DLBCL) N=34, Follicular Lymphoma (FL) N=38, Marginal Zone/Mantle Cell/Chronic Lymphocytic Leukemia (MZL/MCL/CLL) N=12), 20 patients undergoing elective tonsillectomy (tonsil B cells), and 40 healthy volunteers (PB). To enrich for key changes in the NHL epigenome, crosslinked chromatin was subjected to formaldehyde-assisted isolation of regulatory elements (FAIRE), for highly active histone-depleted regions, and chromatin immunoprecipitation (ChIP) for several activating (H3K4me1, H3K27ac, H3K9/14ac), and repressive (H3K27me3) histone marks, followed by high throughput sequencing (FAIRE/ChIP-Seq). To identify genes regulated by putative NHL-specific regulatory elements, we profiled gene expression (mi/mRNA) by microarray and, in primary tumors, by RNA-Seq to detect novel isoforms, translocations, and mutations, such as those in epigenetic modifier genes. In order to analyze this complex dataset, we created a global, integrative algorithm to evaluate the regulatory potential of a given epigenetic element, or set of elements, based on a step-wise approach. All regulatory elements were ranked according to several parameters, including distance to transcription start sites (TSS), gene expression level, chromatin state, distance to CTCF sites, genomic copy number, degree of sequence conservation, association with mutations in epigenetic modifiers, and most importantly, NHL-specificity and recurrence (number of samples). We first established the NHL-specificity of each regulatory element by comparison to matched PBB, if available, or to healthy donor B cells, identifying thousands of regulatory elements that are differentially enriched (“gained” or “lost”) in at least one primary NHL sample. We further assessed the likely role of each element by its genomic, epigenomic, and transcriptomic contexts. Gained elements were significantly associated with higher levels of gene expression in NHL compared to normal B cells (p Disclosures: No relevant conflicts of interest to declare.

Background: Estrogen receptors are over-expressed in around 70% of breast cancer cases. The genetic changes that occur during aromatase inhibitor (AI) treatment are not well understood and may differ depending upon the patient's response phenotype. Methods: We performed whole genome sequencing (WGS) of matched blood, pre-treatment, and post-treatment biopsy samples from 22 estrogen receptor positive breast cancer patients treated with neoadjuvant aromatase inhibitors. For 5 cases, we performed the whole genome sequencing (WGS) on patients’ matched normal, two pre AI-treatment, and two post AI-treatment DNA isolates from biopsy samples. We validated all putative coding and non-coding somatic mutations using deep sequencing. By comparing the validated somatic mutations from pre- and post- AI treatment biopsy samples, we were able to determine the alterations in the tumor genomes. In every case we defined the clonal architecture of each pair of pre-treatment and post-treatment biopsy samples by comparing the variant allele frequencies from thousands of validated somatic mutations. Results: Comparisons of the two pre AI-treatment biopsy samples from the same patient indicates that the variant allele frequencies of mutations showed high concordances in all 5 cases, 0.74 to 0.95 range of correlation coefficient. Only a small percentage of somatic mutations were detected in one pre-treatment sample and not the other (4.65% overall). In comparing the somatic variations between pre-treatment and matched post-treatment biopsy samples in 22 cases, we found that patients with good clinical response to AI treatment retained known driver mutations only in their pre-treatment tumors. Conversely, those patients with poor clinical response presented new driver mutations in their post-treatment samples. Furthermore, the variant allele frequency for most mutated genes decreased in post AI treatment samples for patients with good AI treatment response; on the contrary, the variant allele frequency increased for patients with poor clinical response. Conclusions: From WGS of matched normal, pre-treatment, and post-treatment biopsy samples, we identified new driver genes mutated in patients with poor clinical response, while patients with good clinical response had lost mutated driver genes in their post-treatment biopsy samples. The genetic landscape revealed by WGS of pre-treatment and post-treatment biopsy samples reveals mutational repertoires are remodeled by AI therapy. This finding suggests deep sequencing of AI treated samples will be necessary to reveal the complete complement of mutations present in a patient's tumor. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-423. doi:1538-7445.AM2012-LB-423

Zigzag GaN/Ga2O3 heterogeneous nanowires (NWs) were fabricated, and the optical properties and NO gas sensing ability of the NWs were investigated. We find that NWs are most effective at 850 °C at a switching process once every 10 min (on/off = 10 min per each) with a mixture flow of NH3 and Ar. The red shift of the optical bandgap (0.66 eV) is observed from the UV-vis spectrum as the GaN phase forms. The gas sensing characteristics of the developed sensor are significantly replaced to those of other types of NO sensors reported in literature.

Ti-doped ZnO nanowires (NWs) were fabricated by thermal evaporation and metal vapor vacuum arc (MEVVA) ion implantation process. The effect of Ti doping on the structure, morphology, and electrical/optical properties of the as-grown NWs was investigated. The fraction of Ti doping was estimated to be 1 at. % to 2 at. % based on energy-dispersive x-ray spectroscopy (EDS). The x-ray diffraction analyses indicated that Ti-doped ZnO NWs are similar to ZnO NWs in crystal structure, which has been taken to indicate that no titanium oxide phase was produced. Cathodoluminescence (CL) spectra taken from the Ti-doped ZnO NWs at room temperature showed two distinct emission peaks, at 374 nm and at 752 nm. Electrical measurements showed that the resistivity of a single ZnO NW decreased from 1.22 × 10−1 Ω cm to 3.5 × 10−2 Ω cm with Ti doping. The semiconducting parameters of bent Ti-doped NWs squeezed between two approaching contacts inside the pole piece of the microscope were determined on the basis of experimentally...

Background: Endocrine-therapy resistant HER2 negative luminal-type breast cancer is the commonest cause of breast cancer death but the molecular basis for aggressive clinical behavior is poorly understood. Endocrine therapy resistant cases can be identified early in the course of the disease though the persistant expression of the cell cycle biomarker Ki67 despite neoadjuvant treatment with a potent aromatase inhibitor (JNCI 2008:100;159–61). Methods: Massively parallel DNA sequencing (Nature 2010; 464:999–1005) was applied to samples from two neoadjuvant endocrine trials (“POL” J Am Coll Surg. 2009; 208: 906–14 and “ACOSOG Z1031” JCO in press) to define the whole genome sequence of 50 luminal-type breast cancers (PAM50 definition, JCO 2009;27:1160–7) with an average 30 fold coverage. Of these, 24 were defined as resistant (surgical specimen Ki67 > 10%) and 26 sensitive (Ki67 ≤ 10%). Approximately 10 trillion base pairs of sequence were analyzed. Putative somatic mutations were confirmed through targeted sequence analysis and the absence of the variant in matched normal DNA. Results: The mean number of single nucleotide non-silent variants (SNV) and small deletions (indels) was greater in the resistant group (49 per case) than sensitive cases (23) (p=0.02). The significantly mutated gene list included PIK3CA, TP53, ATR, RUNX1, MYST3, PRSS8, ZNHIT2 and MAP3K1. A large number of structural variations have also been identified with greater than 800 events from 28 patients orthogonally validated to date, mostly deletions but also translocations, although no recurrent translocations have been seen. About 25% of these deletions were paired with an SNV suggesting multiple novel double-hit tumor suppressor events. Extension analysis in 121 POL/Z1031 samples produced the following mutation incidence data PIK3CA (43%), TP53 (15.2%) and MAP3K1 (9.3%). The MAP3K1 mutations were most frequently frame-shift or nonsense, disrupting the C terminal kinase domain, a logical finding in a kinase activated by caspase 7 to promote apoptosis. Only 1 MAP3K1 mutation was observed in 60 basal-like breast cancers (luminal versus basal MAP3K1 mutation frequency p=0.04). Conclusions: MAP3K1is a novel breast cancer tumor suppressor gene more frequently lost in luminal-type than basal-like breast cancer. Further data analysis will be presented including pathway analyses that place less common mutations into a variety of cancer pathways, including phosphoinositol-3-kinase signaling, cell cycle regulation, metabolism, mitotic spindle regulation and DNA mismatch repair. These analyses suggest a classification of the disease that is not based on individual gene abnormalities but common cancer pathway activation events that ultimately determine outcome for patients with luminal-type disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-87. doi:10.1158/1538-7445.AM2011-LB-87