Evaluation of reference genes for qRT-PCR studies in the colchicine producing Gloriosa superba L.

Johnson Nekha,Rodriguez Diaz Diana,Ganapathy Sivakumar,Bass John S.,Kutchan Toni M.,Khan Abdul L.,Flavier Albert B. 한국식물생명공학회 2023 Plant biotechnology reports Vol.17 No.4

The flame lily, Gloriosa superba L., is one of the two primary sources of the anti-inflammatory drug, colchicine. Previous studies have shown that a higher level of colchicine production occurs in the rhizomes than in leaves and roots. Earlier precursor feeding and transcriptome analysis of G. superba have provided a putative pathway and candidate genes involved in colchicine biosynthesis. Comparative analysis of expression levels of candidate pathway genes in different tissues of G. superba using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) can reveal highly expressed genes in the rhizome compared to other tissues which could suggest roles of the gene products in colchicine biosynthesis. Normalization is an important step in effectively analyzing differential gene expression by qRT-PCR with broader applications. The current study selected candidate reference genes from the transcriptome datasets and analyzed them to determine the most stable genes for normalization of colchicine biosynthesis-related genes. Using RefFinder, one stable reference gene, UBC22, was selected to normalize gene expression levels of candidate methyltransferase (MT) genes in the leaves, roots, and rhizomes of G. superba. With UBC22 as reference gene, the methyltransferases, GsOMT1, GsOMT3, and GsOMT4 showed significantly higher expression levels in the rhizome of G. superba, while MT31794 was more highly expressed in the roots. In conclusion, the current results showed a viable reference gene expression analysis system that could help elucidate colchicine biosynthesis and its exploitation for increased production of the drug in G. superba.

A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

Chen, Han,Li, Chunyan,Peng, Xinxin,Zhou, Zhicheng,Weinstein, John N.,Caesar-Johnson, Samantha J.,Demchok, John A.,Felau, Ina,Kasapi, Melpomeni,Ferguson, Martin L.,Hutter, Carolyn M.,Sofia, Heidi J.,Ta Elsevier 2018 Cell Vol.173 No.2

<P><B>Summary</B></P> <P>The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on “chromatin-state” to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Systematic analysis of enhancer expression across ∼9,000 samples of 33 cancer types </LI> <LI> Global enhancer activation positively correlates with aneuploidy but not mutations </LI> <LI> A computational method that infers causal enhancer-target-gene relationships </LI> <LI> Enhancers as key regulators of therapeutic targets, including PD-L1 </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>

Complementary neutron and x-ray reflectivity studies of “near-frictionless” carbon films

Johnson, Jacqueline A.,Park, Sungkyun,Roy, Sujoy,Sinha, Sunil K.,Erdemir, Ali,Eryilmaz, Osman L.,Woodford, John B. American Institute of Physics 2007 JOURNAL OF APPLIED PHYSICS - Vol.101 No.12

Genetic variation at <i>CYP3A</i> is associated with age at menarche and breast cancer risk: a case-control study

Johnson, Nichola,Dudbridge, Frank,Orr, Nick,Gibson, Lorna,Jones, Michael E,Schoemaker, Minouk J,Folkerd, Elizabeth J,Haynes, Ben P,Hopper, John L,Southey, Melissa C,Dite, Gillian S,Apicella, Carmel,Sc BioMed Central 2014 Breast cancer research Vol.16 No.3

<P><B>Introduction</B></P><P>We have previously shown that a tag single nucleotide polymorphism (rs10235235), which maps to the <I>CYP3A</I> locus (7q22.1), was associated with a reduction in premenopausal urinary estrone glucuronide levels and a modest reduction in risk of breast cancer in women age ≤50 years.</P><P><B>Methods</B></P><P>We further investigated the association of rs10235235 with breast cancer risk in a large case control study of 47,346 cases and 47,570 controls from 52 studies participating in the Breast Cancer Association Consortium. Genotyping of rs10235235 was conducted using a custom Illumina Infinium array. Stratified analyses were conducted to determine whether this association was modified by age at diagnosis, ethnicity, age at menarche or tumor characteristics.</P><P><B>Results</B></P><P>We confirmed the association of rs10235235 with breast cancer risk for women of European ancestry but found no evidence that this association differed with age at diagnosis. Heterozygote and homozygote odds ratios (ORs) were OR = 0.98 (95% CI 0.94, 1.01; <I>P</I> = 0.2) and OR = 0.80 (95% CI 0.69, 0.93; <I>P</I> = 0.004), respectively (<I>P</I><SUB>trend</SUB> = 0.02). There was no evidence of effect modification by tumor characteristics. rs10235235 was, however, associated with age at menarche in controls (<I>P</I><SUB>trend</SUB> = 0.005) but not cases (<I>P</I><SUB>trend</SUB> = 0.97). Consequently the association between rs10235235 and breast cancer risk differed according to age at menarche (<I>P</I><SUB>het</SUB> = 0.02); the rare allele of rs10235235 was associated with a reduction in breast cancer risk for women who had their menarche age ≥15 years (OR<SUB>het</SUB> = 0.84, 95% CI 0.75, 0.94; OR<SUB>hom</SUB> = 0.81, 95% CI 0.51, 1.30; <I>P</I><SUB>trend</SUB> = 0.002) but not for those who had their menarche age ≤11 years (OR<SUB>het</SUB> = 1.06, 95% CI 0.95, 1.19, OR<SUB>hom</SUB> = 1.07, 95% CI 0.67, 1.72; <I>P</I><SUB>trend</SUB> = 0.29).</P><P><B>Conclusions</B></P><P>To our knowledge rs10235235 is the first single nucleotide polymorphism to be associated with both breast cancer risk and age at menarche consistent with the well-documented association between later age at menarche and a reduction in breast cancer risk. These associations are likely mediated via an effect on circulating hormone levels.</P>

PULMONARY RETENTION OF INHALED SUBMICRON PARTICLES IN RATS: Diesel Exhaust Exposures and Lung Retention Model

Tai L.Chan,John T.Johnson 한국자동차공학회 1987 한국자동차공학회 학술강연초록집 Vol.- No.-

Unified Molding and Simulation for Nano-structured Tungsten Carbide

Park Seong-Jin,Johnson John L.,German Randall M. 한국분말야금학회 2006 한국분말야금학회 학술대회논문집 Vol.2006 No.1

Nano-structured tungsten carbide compacts with cobalt matrices (WC-Co) offer new opportunities for achieving superior hardness and toughness combinations. A unified modeling and simulation tool has been developed to produce maps of sintering pathways from nanocrystalline WC powder to sintered nano-structured WC-Co compacts. This tool includes (1) die compaction, (2) grain growth, (3) densification, (4) sensitivity analysis, and (5) optimization. All material parameters were obtained by curve fitting based on results with two WC-Co powders. Critical processing parameters are determined based on sensitivity analysis and are optimized to minimize grain size with high density.

COLLABORATION WITH HIGHER EDUCATION INSTITUTIONS (HEIs) FOR SUCCESSFUL FIRM INNOVATION

Hakil Moon,Babu John Mariadoss,Jean L. Johnson 글로벌지식마케팅경영학회 2016 Global Marketing Conference Vol.2016 No.7

Introduction Shorter innovation cycles, the huge cost of R&D and dearth of resources compel firms to search for new innovation sources (Gassmann and Enkel 2004). Current research argues that firms need to open up their solid boundaries and seek valuable knowledge from external partners so that firms can extend the innovation function beyond their four walls (Chesbrough 2003). In this context past research has identified universities, or higher education institutions (HEIs) as an important source of innovation (e.g., Lambert 2003). Indeed, universities undertake a “third mission” in addition to their core mission of research and teaching, by focusing on “technology transfer” that engages in the process of the commercialization of science (Etzkowitz et al. 2000). Thus, firms can take huge advantages through the collaboration with universities. While relationships between firms have the risk of opportunism embedded in them, support provided by universities are hard to imitate by competitors due to the novelty and uniqueness in the ideas they provide their partner firms. Despite this important role that universities play, no systematic theoretical treatment has been attempted in academia. Ironically, university and industry links have been studied much less frequently and have been valued lesser than other sources (e.g., suppliers and customers) in terms of knowledge transfer for firm innovation (Hughes 2011). Extant research examines collaborations between universities and firms using simple descriptive analysis (e.g., Laursen and Salter 2004) and illustrates the relationship with anecdotal evidence (e.g., Cosh and Hughes 2010). Thus, extant literature provides little-to-no empirical evidence regarding firm performance, such as a firm’s innovation outcomes, when the firms are supported by universities. Our broad-based investigation makes several key contributions. First, our study is the first to demonstrate empirically what types of HEIs’ activities enhance a firm’s innovation outcomes. Because the two different types of HEI activities have different features, it helps us get a more precise understanding of which specific type of HEI-supported activity influences which firm innovation outcome. Second, our research finds that a firm’s absorptive capacity influences the relationship between HEI-supported activities and a firm’s innovation outcomes. This finding helps to identify how firm capability to absorb outside knowledge influences the relationship of HEIs’ involvement on a firm’s innovation outcomes. Conceptual Framework The most frequent form of a firm’s interaction with universities is people-based activities (Hughes 2011). Universities transfer knowledge through people-related activities such as conferences, special lectures, education programs, and social networks supporting firm innovation. Such people-based activities can influence firm innovation performance. People-based activities involve the activities conducting by firms to increase their business competitiveness. Since a firm’s employees are key to discovering new products and processes, special training programs provided by universities will help supplementing knowledge towards specific firm innovation outcomes. Additionally, other people-related activities such as placing university staff on a firm’s board of directors can also encourage exchange of knowledge and information resulting in cutting-edge new product and process innovation. Tether and Tajar (2008) found that firms that have participated in professional meetings or conferences held by HEIs have a better chance of surpassing their current innovation performance. A firm can improve its innovation performance by making human assets supported by its partners. As partners work together, this helps increasing work efficiency by improving communication, knowledge sharing, and their relative capacity to absorb knowledge for innovation. Research suggests that universities may have lower barriers to engagement with firms by removing bureaucracy, lowering transaction costs and speeding up reaction times (Mateos-Garcia and Sapsed 2011). Therefore, universities have an important role in transferring new knowledge through people-based activities, resulting in new products and processes for the firm. Thus, we hypothesize as follows: Hypothesis 1A (H1A). A firm’s people-based activities with HEIs are positively related to the introduction of new products in the firm. Hypothesis 1B (H1B). A firm’s people-based activities with HEIs are positively related to the introduction of new processes in the firm. Universities have a distinct role in affecting a firm’s innovation performance through problem-solving activities. Firms that acquire knowledge from universities improve their competitive position that helps firm acquire a competitive advantage over other firms that do not collaborate with universities (Gassmann and Enkel 2004). Universities provide problem-solving activities such as joint research, contract research, consulting services, informal advice and provision of access to specialized instrumentation, equipment or materials and of product prototyping. For example, in 2009, US firms sponsored more than $4 billion worth of university research (Kurman 2011), as a result of which U.S. universities own nearly one-quarter of new U.S. patents in the fields of nanotechnology and biotechnology. Thus, firms that collaborate with universities can achieve cutting-edge product and process innovation (Kurman 2011). Hosting workshops and performing joint research with universities are core problem-solving activities. For example, IBM, one of the most successful and established enterprises in the IT market, hosted 350 workshops per year and has had 50-100 ongoing research projects with universities, helping IBM to successfully launch new products into the market (Gassmann and Enkel 2004). Further, firms can also integrate partners (i.e., HEIs) to combine their different competencies to enrich their own innovation process (Gassmann and Enkel 2004). Based on the above, we hypothesize as follows:Hypothesis 2A (H2A). A firm’s problem-solving activities with HEIs are positively related to the introduction of new products. Hypothesis 2B (H2B). A firm’s problem-solving activities with HEIs are positively related to the introduction of new processes. Shorter time-to-market strategies, increasing R&D costs and a dearth of resources cause firms to search for new innovation strategies. This phenomenon is reinforced by a rapid churn in technology and customer demands. In this competitive environment, HEIs’ involvement is increasingly important for a firm’s innovation success because integrating external sources of knowledge from HEIs can result in major advantages for firms (Rappert et al. 1999). Further, people-based and problem-solving activities supported by HEIs do not replace a firm’s internal innovation activities and, as a result, the firm undertakes a great deal of its own innovation activities. Also, scholars argue that collaboration with other partners does not always provide better innovation performance because of the lack of a firm’s capability to processing valuable knowledge from the outside partners (Cohen and Levinthal 1990). This indicates that the mere acquisition and exploitation of knowledge from universities do not guarantee successful firm innovation outcomes. To create successful firm innovation, the firm should possess absorptive capacity, which is the learning capability to processing knowledge acquired from the HEIs into their internal work. Thus, firms can be expected to invest in their absorptive capacity in this situation (Tether and Tajar 2008). Further, Keller (1996) argues that successful R&D spillover (i.e., absorptive capacity) effects are dependent on the activities of human capital (i.e., people-based activities). Also, Cohen and Levinthal (1990) argue that firms can increase their absorptive capacity directly, as when they send personnel for advance technical training (i.e., people-based activities). Further, Kim (1998) argues that absorptive capacity is the major factor in developing problem-solving skills that allow a firm to create new knowledge that influences firm innovation performance. As such, absorptive capacity stresses the internal capability to acquire and assimilate outside knowledge into a firm while HEIs’ involvement is a resource that is created by external source enhancing a firm’s innovation outcomes. Therefore, identifying the role of absorptive capacity is a useful tool to explain the relationship of HEIs’ people-based activities and problem-solving activities on firm innovation performance. However, Nooteboom and colleagues (2007, pp. 1031) argue that “while there may be increasing returns in absorptive capacity, improving the general ability to understand and appreciate novelty value in collaboration, there are decreasing returns to knowledge in finding further novelty: the more one knows the further away one has to look for novelty.” This indicates that too much absorptive capacity in a firm negatively affects the impact of people-based activities on a firm’s innovation performance. While people attending conferences or lectures supported by universities may acquire novel knowledge that can influence a firm’s innovation performance, their activities may have negative impact on a firm’s innovation outcomes when a firm has greater absorptive capacity, due to diminishing impact of a firm’s absorptive capacity to create novel idea. Extant research suggests that the greater a firm’s absorptive capacity, the lesser the firm can find further novelty (Noteboom et al. 2007), which suggests that absorptive capacity makes firm innovation activities less efficient. Based on the above discussion, we hypothesize as follows:Hypothesis 3A (H3A). People-based activities with HEIs positively related to the introduction of new products and/or processes will become weaker at a higher level of absorptive capacity. Hypothesis 3B (H3B). People-based activities with HEIs positively related to new product radicalness will become weaker at a higher level of absorptive capacity. Hypothesis 4A (H4A). Problem-solving activities with HEIs positively related to the introduction of new products and/or processes will become stronger at a higher level of absorptive capacity. Hypothesis 4B (H4B). Problem-solving activities with HEIs positively related to new product radicalness will become stronger at a higher level of absorptive capacity. Methods We test the hypotheses presented across two studies. The purpose of Study 1 is to validate our prediction about how HEI activities affect firm innovation performance (H1A to H2B). Study 2 expands this initial research frame by validating the moderating effects of a firm’s absorptive capacity on firm innovation outcomes (H3A to H4B). Implications There is an argument to transfer knowledge from HEIs to firms due to the cultural differences between them (Lambert 2003). Nevertheless, universities are playing an increasingly strategic role in stimulating innovation in firms though the transfer of technology (Hughes 2011). Scholars have largely disregarded the more specific activities performed by HEIs such as people-based and problem-solving activities. Little attention has been paid to how people-based and problem-solving activities affect firm innovation performance. Further, firm innovation outcomes can be affected differently by some specific HEI activities because each activity supported by HEIs plays a different role in impacting certain types of firm innovation outcomes. Based on our results, problem-solving activities are related to new product innovation while people-based activities are related to new process innovation. Additionally, absorptive capacity had a negative moderating effect with people based activities and a positive moderating effect with problem solving activities on a firm’s innovation outcomes. This is important to theoretical and practical implications because a firm is able to know which activities are required to improve their new product or process innovation. This leads a firm to save huge costs to achieve successful innovation.

Development of Nano-Tungsten-Copper Powder and PM Processes

Lee Seong,Noh Joon-Woong,Kwon Young-Sam,Chung Seong-Taek,Johnson John L.,Park Seong-Jin,German Randall M. 한국분말야금학회 2006 한국분말야금학회 학술대회논문집 Vol.2006 No.1

Thermal management technology is a critical element in all new chip generations, caused by a power multiplication combined with a size reduction. A heat sink, mounted on a base plate, requires the use of special materials possessing both high thermal conductivity (TC) and a coefficient of thermal expansion (CTE) that matches semiconductor materials as well as certain packaging ceramics. In this study, nano tungsten coated copper powder has been developed with a wide range of compositions, 90W-10Cu to 10W-90Cu. Powder technologies were used to make samples to evaluate density, TC, and CTE. Measured TC lies among theoretical values predicted by several existing models.

Fine-mapping identifies two additional breast cancer susceptibility loci at 9q31.2

Orr, Nick,Dudbridge, Frank,Dryden, Nicola,Maguire, Sarah,Novo, Daniela,Perrakis, Eleni,Johnson, Nichola,Ghoussaini, Maya,Hopper, John L.,Southey, Melissa C.,Apicella, Carmel,Stone, Jennifer,Schmidt, M IRL Press 2015 Human molecular genetics Vol.24 No.10

<P>We recently identified a novel susceptibility variant, rs865686, for estrogen-receptor positive breast cancer at 9q31.2. Here, we report a fine-mapping analysis of the 9q31.2 susceptibility locus using 43 160 cases and 42 600 controls of European ancestry ascertained from 52 studies and a further 5795 cases and 6624 controls of Asian ancestry from nine studies. Single nucleotide polymorphism (SNP) rs676256 was most strongly associated with risk in Europeans (odds ratios [OR] = 0.90 [0.88–0.92]; <I>P</I>-value = 1.58 × 10<SUP>−25</SUP>). This SNP is one of a cluster of highly correlated variants, including rs865686, that spans ∼14.5 kb. We identified two additional independent association signals demarcated by SNPs rs10816625 (OR = 1.12 [1.08–1.17]; <I>P</I>-value = 7.89 × 10<SUP>−09</SUP>) and rs13294895 (OR = 1.09 [1.06–1.12]; <I>P</I>-value = 2.97 × 10<SUP>−11</SUP>). SNP rs10816625, but not rs13294895, was also associated with risk of breast cancer in Asian individuals (OR = 1.12 [1.06–1.18]; <I>P</I>-value = 2.77 × 10<SUP>−05</SUP>). Functional genomic annotation using data derived from breast cancer cell-line models indicates that these SNPs localise to putative enhancer elements that bind known drivers of hormone-dependent breast cancer, including ER-α, FOXA1 and GATA-3. <I>In vitro</I> analyses indicate that rs10816625 and rs13294895 have allele-specific effects on enhancer activity and suggest chromatin interactions with the <I>KLF4</I> gene locus. These results demonstrate the power of dense genotyping in large studies to identify independent susceptibility variants. Analysis of associations using subjects with different ancestry, combined with bioinformatic and genomic characterisation, can provide strong evidence for the likely causative alleles and their functional basis.</P>

lncRNA Epigenetic Landscape Analysis Identifies <i>EPIC1</i> as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

Wang, Zehua,Yang, Bo,Zhang, Min,Guo, Weiwei,Wu, Zhiyuan,Wang, Yue,Jia, Lin,Li, Song,Caesar-Johnson, Samantha J.,Demchok, John A.,Felau, Ina,Kasapi, Melpomeni,Ferguson, Martin L.,Hutter, Carolyn M.,Sof Cell Press 2018 Cancer Cell Vol. No.

<P><B>Summary</B></P> <P>We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, we observed a recurrent hypomethylation of 1,006 lncRNA genes in cancer, including <I>EPIC1</I> (epigenetically-induced lncRNA1). Overexpression of <I>EPIC1</I> is associated with poor prognosis in luminal B breast cancer patients and enhances tumor growth <I>in vitro</I> and <I>in vivo.</I> Mechanistically, <I>EPIC1</I> promotes cell-cycle progression by interacting with MYC through <I>EPIC1</I>'s 129–283 nt region. <I>EPIC1</I> knockdown reduces the occupancy of MYC to its target genes (e.g., <I>CDKN1A</I>, <I>CCNA2</I>, <I>CDC20</I>, and <I>CDC45</I>). MYC depletion abolishes <I>EPIC1</I>'s regulation of MYC target and luminal breast cancer tumorigenesis <I>in vitro</I> and <I>in vivo</I>.</P> <P><B>Highlights</B></P> <P> <UL> <LI> LncRNAs show a hypomethylation phenotype, in contrast to a CIMP phenotype in cancer </LI> <LI> <I>EPIC1</I> promotes breast tumorigenesis through regulating cancer cell-cycle progression </LI> <LI> <I>EPIC1</I> directly interacts with MYC protein through <I>EPIC1</I>'s 129–283 nt region </LI> <LI> <I>EPIC1</I> regulates MYC targets by enhancing MYC occupancy on its target promoters </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>