bluuebunny/crossref_metadata_2025_split huggingface dataset:
FRACTAL ANALYSIS OF LIPASE–CATALYSED SYNTHESIS OF BUTYL BUTYRATE IN A MICROBIOREACTOR UNDER THE INFLUENCE OF NOISE
Authors: PATNAIK PRATAP R. 
Published: April 2013

Microbioreactors operated in real environments are often subject to noise from the environment. This is commonly manifested as fluctuations in the flow rates of the feed streams. Previous studies with larger bioreactors have shown that noise can seriously impair the performance. Given this possibility, the effects of noise on the performance of a microbioreactor have been analyzed for the trans-esterification of vinyl butyrate by 1-butanol by immobilized lipase B to produce butyl butyrate. As in previous work for macrobioreactors, the analysis was done with (i) no noise, (ii) unfiltered noise, and (iii) noise filtered by four different methods, and the fractal dimension of the product was used as an index of the performance. All fractal dimensions decreased with increasing dilution rates, and significant stochastic chaos was likely at low dilution rates. Of the four types of filters, the auto-associative neural filter (ANF) was the most effective in reducing chaos and restoring of smooth, nearly noise-free performance. The ANF also does not require a process model, which is a significant advantage for real systems. Simulations also revealed that even in the absence of noise, deterministic chaos is possible at low dilution rates; this underscores the importance of efficient filtering under such conditions when external noise too is present. The results thus establish the importance of noise in microbioreactor behavior and the usefulness of the fractal dimension in characterizing the effects.
Sequential Inhibitor Therapy in CML: In Vitro Simulation Elucidates the Pattern of Resistance Mutations after Second- and Third-Line Treatment
Authors: Bauer Robert C. , Sänger Jana , Peschel Christian , Duyster Justus , von Bubnoff Nikolas 
Published: April 2013

Abstract
Purpose: Dasatinib and nilotinib are active in imatinib-resistant chronic myelocytic leukemia (CML) and many patients undergo sequential treatment. We aimed at modeling sequential tyrosine kinase inhibitor (TKI) resistance in vitro to compare the sequences imatinib-nilotinib-dasatinib and imatinib-dasatinib-nilotinib.
Experimental Design: We designed an in vitro model for sequential TKI resistance in CML. Replicates of imatinib-resistant cell lines were treated with dasatinib or nilotinib. Second-line resistant replicates were exposed to third-line treatment.
Results: Growth of all replicates in all three lines of treatment was associated with T315I. However, T315I occurred with low abundance and did not increase during sequential treatment. Nilotinib second-line more often gave rise to sequential resistance compared with dasatinib due to pre-existing P-loop mutations, especially at suboptimal drug concentration. In contrast, mutations predisposing to dasatinib resistance such as F317C/V and V299L did not occur before dasatinib exposure. Nilotinib third-line did not overcome imatinib-dasatinib resistance due to pre-existing T315I or P-loop/V299L or P-loop/F317 exchanges. Dasatinib third-line suppressed imatinib-nilotinib–resistant replicates with residual sensitivity.
Conclusions: Sequential acquisition of BCR-ABL drug resistance mutations in CML might be underestimated. Resistance to sequential TKI monotherapy in vitro more often was associated with stepwise acquisition of drug-specific compound mutations compared with T315I. Pre-existing mutations strongly limited the activity of both third-line treatments, and the activity of nilotinib second-line in vitro critically depended on drug concentration. Clin Cancer Res; 19(11); 2962–72. ©2013 AACR.
Abstract A1: Long stress-induced non-coding transcripts (LSINCTs) and Cancer
Authors: Smith David I. , Jessica Silva M. 
Published: April 2013

Abstract
We previously utilized a whole genome tiling array to identify novel transcripts which had altered expression in response to the genotoxic effects of the tobacco carcinogen NNK. Our goal was to identify novel long stress-induced non-coding transcripts that could play important regulatory roles within cells and be important targets of alteration during cancer formation. Utilizing very stringent criteria, we examined all transcriptionally active regions that had altered expression in response to NNK treatment and identified a group of 12 transcripts, termed long stress-induced noncoding trancripts (LSINCTs). These novel long non-coding transcripts are between 2 and 4 Kb in length and do not contain any open reading frames or have homology to any mRNAs. 11 LSINCTs are intergenically located and one LSINCT is intragenically located within the genome. We found LSINCTs to be more highly expressed in more proliferative normal human tissues and to be frequently over-expressed in a number of different cancers including breast cancer. We studied one of these transcripts in greater detail, LSINCT5. We found LSINCT5 to be a polyadenylated nuclear transcript of exactly 2,647 base pairs. It is highly over-expressed in both breast and ovarian cancers and knocking down its' expression in either a breast or ovarian cancer cell line resulted in decreased cellular proliferation. We further compared gene expression in the breast cancer cell line, MCF7, before and after knocking down LSINCT5 expression and identified a number of genes whose expression changed more than 2-fold in response. Two of the genes identified were the gene for the major paraspeckle protein PSPC1, and another long non-coding transcript NEAT1. Paraspeckles are irregularly shaped compartments found in the nucleus' interchromatin space. Paraspeckles are RNA-protein structures formed by the interaction of NEAT1 and members of the Drosophila Behavior Human Splicing family of proteins including PSPC1. Paraspeckles appear to be critical to the control of gene expression through the nuclear retention of certain species of RNA. It is though that paraspeckles and their components play a role in controlling gene expression during a number of different cellular processes including differentiation, viral infection and stress responses. Using RNA fluorescent in situ hybridization, we found LSINCT5 to co-localize with NEAT1 within the nucleus. Hence, this novel stress-induced transcript may be another important long non-coding transcript that is involved in the normal cellular function of the paraspeckles.
Citation Format: David I. Smith, Silva M. Jessica. Long stress-induced non-coding transcripts (LSINCTs) and Cancer [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A1.
Abstract A17: MiR-15, miR-16 and miR-21 are direct transcriptional targets of E2F1 that limit E2F-induced proliferation and apoptosis
Authors: Ofir Matan , Ben-Shachar Berta , Hacohen Dalia , Ginsberg Doron 
Published: April 2013

Abstract
microRNAs (miRs) are small non-coding RNA molecules that have recently emerged as critical regulators of gene expression and are often deregulated in cancer. In particular, miRs encoded by the miR-15a, miR-16-1 cluster are frequently deleted in certain cancers and appear to act as tumor suppressors. Furthermore, miR-21 is over-expressed in a wide variety of human tumors and functions as an oncogene. Here, we provide evidence that miR-21, the miR-15a, miR-16-1 cluster and related miR-15b, miR-16-2 cluster comprise miRs regulated by E2F1, a pivotal transcription factor that can induce both proliferation and cell death. E2F1 is a critical downstream target of the tumor suppressor RB. The retinoblastoma pathway is often inactivated in human tumors resulting in deregulated E2F activity. We show that expression levels of the five mature miRs, miR-15a, miR-16-1, miR-15b, miR-16-2 and miR-21 are elevated upon activation of ectopic E2F1. Moreover, activation of endogenous E2Fs up-regulates expression of these miRs and endogenous E2F1 binds their respective promoters.
Importantly, we corroborate that miR-15a/b inhibits expression of cyclin E, a key direct transcriptional target of E2F pivotal for the G1/S transition. Similarly, miR-21 inhibits the expression of the pro-apoptotic tumor suppressor gene maspin, another direct transcriptional target of E2F. Therefore, our data suggest the existence of feed forward loops that modulate E2F activity and consist of E2F1; E2F1-regulated miRs -miR-15 and miR-21; and E2F1-regulated genes-cyclin E and maspin. In support of this, ectopic expression of miR-15 inhibits G1/S transition and, conversely, inhibition of miR-15 expression enhances E2F1-induced G1/S transition and up-regulation of cyclin E levels. Also, inhibition of miR-21 expression enhances E2F1-induced up regulation of maspin, as well as E2F1-mediated apoptosis.
In summary, our data identify miR-15, miR-16 and miR-21 as novel transcriptional targets of E2F that, in turn, modulate E2F activity.
Citation Format: Matan Ofir, Berta Ben-Shachar, Dalia Hacohen, Doron Ginsberg. MiR-15, miR-16 and miR-21 are direct transcriptional targets of E2F1 that limit E2F-induced proliferation and apoptosis [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A17.
Abstract A19: Profiling long noncoding RNA expression in cancer cells by real-time PCR arrays
Authors: Wu Fangting , Mo Yin-Yuan 
Published: April 2013

Abstract
Long noncoding RNAs (lncRNAs), as a new class of transcripts, have been recently shown to be pervasively transcribed in the genomes of human and mouse. In particular, accumulating evidence link the expression of lncRNAs to diverse human diseases, highlighting their potential as biomarkers and therapeutic targets. However, there are still many missing dots in our current understanding of lncRNA function. Thus, investigation of the expression patterns of lncRNAs is a crucial step to understanding of their roles in many model systems. To this end, we developed a qPCR based disease-related human lncRNA profiler, which allows for the quantification of differential expression of 83 individual lncRNAs among various experimental RNA samples. All 83 lncRNAs chosen for the array are based on publications and they are implicated in diseases ranging from neurodegeneration to cancer. The array plate also includes the house keeping genes and small RNA transcripts for normalization purposes. To determine the utility of this lncRNA profiler, we profiled their expression in breast cancer specimens compared to matched normal tissue and identified several lncRNAs are dysregulated, suggesting that lncRNAs may function as oncogenes or tumor suppressors. Gene expression profiling with this lncRNA profiler in a series of breast cell lines such as MCF10A, MCF7 and MDA-MB-231 cells identified differential expression patterns unique to each cell line, which may provide a basis for future analysis of these differentially expressed lncRNAs. Furthermore, we determined the effect of p53 on lncRNA expression in HCT-116 and MCF-7 cells. Initial testing indicated that at least three lncRNAs are induced by p53 in both cell lines. Experiments are underway to further characterize these p53 inducible lncRNAs. Together, these results suggest that disease-related human lncRNA profiler is a valuable research tool that can be tailored for specific needs in different research laboratories. The features of this profiler are easy, convenient, sensitive and specific. Accordingly it serves the first step toward the understanding of the role of lncRNAs in human diseases.
Citation Format: Fangting Wu, Yin-Yuan Mo. Profiling long noncoding RNA expression in cancer cells by real-time PCR arrays [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A19.
Abstract A21: MALAT-1 is essential for lung cancer metastasis in a novel human knockout model
Authors: Gutschner Tony , Eißmann Moritz , Hämmerle Monika , Stentrup Marion , Hildenbrandt Catherina , Groß Matthias , Zörnig Martin , Diederichs Sven 
Published: April 2013

Abstract
The highly conserved long non-coding RNA MALAT-1 (Metastasis-Associated in Lung Adenocarcinoma Transcript 1) had been discovered as a prognostic marker associated with poor survival and development of distant metastasis in lung adenocarcinoma. Since then, it has been found to be deregulated in numerous tumor entities and has been linked to splicing. However, its functional relevance in tumor cells remains to be elucidated. Knockdown models for MALAT1 have been described but suffer from insufficient silencing efficiency of the highly abundant, nuclear non-coding RNA (ncRNA).
In this project, we have developed a novel strategy to create ncRNA knockouts in human cancer cell lines. We have successfully used a synthetic Zinc Finger Nuclease engineered to target the 5′-region of MALAT1 to stably and biallelically integrate RNA-destabilizing elements into the genome of human lung cancer cells (A549). This approach resulted in a specific and more than 1000-fold silencing of MALAT1 in individual clones compared to a less than 5-fold silencing using siRNAs. Thus, this approach can be used to create functional knockouts of coding as well as non-coding genes also in human tumor cell lines allowing loss-of-function studies also of non-conserved ncRNAs in the future.
Phenotypically, the MALAT1-Knockout cells (KO) greatly differ from their parental cell line and wildtype clones (WT): Next to morphological changes, the migration of the KO cells is largely impaired as shown in scratch assays. In xenograft assays after i.v. injection, the KO cells form significantly fewer and smaller lung metastases than their WT counterparts. Since no large difference was observed after subcutaneous injection of the WT and the KO cells, this indicates a specific, active and essential function of MALAT1 in metastasis.
Exon microarrays of the WT and KO cell lines have revealed multiple migration- or metastasis-associated transcripts deregulated by loss of MALAT1 and hence potential target genes. These analyses also uncovered, that splicing is likely not the only functional mechanism of MALAT1 in the nucleus.
Taken together, we have developed a novel, highly effective approach for the knockout of genes that can be used for non-coding as well as coding RNAs in human tumor cells as well as cells from other species. Knockout of MALAT1 in human lung cancer cells revealed its essential function in metastasis as well as genes directly and indirectly targeted by MALAT1.
Citation Format: Tony Gutschner, Moritz Eißmann, Monika Hämmerle, Marion Stentrup, Catherina Hildenbrandt, Matthias Groß, Martin Zörnig, Sven Diederichs. MALAT-1 is essential for lung cancer metastasis in a novel human knockout model [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A21.
Abstract A24: Interaction of miR-106a~363Xpcl1 and p27Kip1 in thymopoiesis and lymphomagenesis
Authors: Kuppers Daniel , Schmitt Thomas , Clurman Bruce , Hwang Harry , Fero Matthew L. 
Published: April 2013

Abstract
The Xpcl1 (Kis2) gene encodes the miR-106a~363 miRNA cluster in mice. Although it was first identified as common integration site of the M-MuLV retrovirus in tumors from p27Kip1 (Cdkn1b) knockout mice, the nature of its interaction with cell cycle genes is uncertain. The miR-106a~363 miRNAs are highly conserved across species, implying an important role in normal biological processes. However, in the absence of a reported phenotype in knockout mice, its normal function is unclear. We examined miR-106a~363 expression in developing T lymphocytes and found that it is highly expressed in immature T-cells but is repressed at the CD4+/CD8+ double positive (DP) stage of thymopoiesis. Using a T cell specific Xpcl1 transgene, we found that forced expression of miR-106a~363 altered the distribution of T cell subsets. Xpcl1 repressed T-cell receptor expression and directly targeted the CD69 cell surface protein. This causes accumulation of DP thymocytes through complementary mechanisms.
We show that, in developing T-cells, p27Kip1 is differentially regulated due to variation in expression of FoxO family transcription factors. Likewise, p27 is upregulated at the transcriptional level by Xpcl1, which is surprising since this should have a tumor suppressor effect. Nonetheless, miR-106a~363 transgenic (Lx) mice developed spontaneous high grade T cell lymphomas. The combination of p27Kip1 deletion with miR-106a~363 overexpression, markedly accelerated lymphoma development, confirming cooperation of these two mutations. We conclude that deletion of p27Kip1 directly overcomes a tumor-suppressor activity of miR-106a~363, whereas the principal oncogenic function of the miRNA cluster remains unknown.
Citation Format: Daniel Kuppers, Thomas Schmitt, Bruce Clurman, Harry Hwang, Matthew L. Fero. Interaction of miR-106a~363Xpcl1 and p27Kip1 in thymopoiesis and lymphomagenesis [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A24.
Abstract A5: Cytotoxic Extracts of Ethnomedicinal Plants: Podophyllum peltatum (Mayapple) and Echinacea angustifolia
Authors: James Olena T. , Myles E. Lewis 
Published: April 2013

Abstract
Phytochemical and other natural compounds are historically established as cures for many ailments in rural America and other developing countries. Our lab is testing plants that show potential for inhibiting the growth of cancer cells. The family Asteraceae and the family Berberidacae are very well known for their values as medicinal plants. More specifically, the genus species Echinacea angustifolia and genus species Podophyllum peltatum commonly known as the Mayapple, both are noted for their unique medicinal purposes. The crude methanol extracts of these plants were tested against human metastatic cell lines representing breast (MCF-7), (BT-549) and colon (SW620) tissues. Trypan blue exclusion is used to determine viable cell counts. Alamar BlueTM and florescent analysis were used to evaluate the cytoxicity of the extracts. Analysis of the crude extracts of Echinacea angustifolia has shown on MCF-7, BT-549, and SW620 that most of them exhibit anticancer activity against the cell lines at the maximum concentration of 200 μg/mL. In particular, less diluted concentrations have demonstrated exceptional inhibitory effects with IC50 values ranging between 0.10–15 μg/mL, respectively. On the other hand, analysis of the crude extracts of Podophyllum peltatum (Mayapple) has shown on MCF-7, BT-549 and SW620 some anticancer activity against cell lines at the maximum concentration of 200 μg/mL. More specifically, the more diluted concentrations have demonstrated exceptional growth inhibition with IC50 values ranging between 2–8 μg/mL
Citation Format: Olena T. James, E. Lewis Myles. Cytotoxic Extracts of Ethnomedicinal Plants: Podophyllum peltatum (Mayapple) and Echinacea angustifolia [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A5.
Abstract A7: Roles of miRNAs in the switch of TGF-β from tumor suppressor to pro-oncogenic factor in cancer progression
Authors: Nagano Yoshiko , Lee Maxwell P. , Wakefield Lalage M. 
Published: April 2013

Abstract
TGF-β is a widely expressed pleiotropic growth factor that plays complex roles in tumorigenesis. TGF-β switches from tumor suppressor to pro-oncogenic factor during breast cancer progression. Our goal is to identify molecular determinants of the TGF-β switch. Since miRNA expression is deregulated in cancer, and TGF-β is reported to regulate expression and biogenesis of miRNAs, we hypothesize that miRNAs may contribute to this switch. To model the TGF-β switch, we used a series of human breast cancer cell lines derived from the spontaneously immortalized MCF10A human breast epithelial cell line. The model consists of 4 cell lines. In the MCF10A (M-I; normal), MCF10AT (M-II; premalignant) and MCF10CA1hcl4 (M-IIIcl4; low-grade tumor) lines, TGF-β is a tumor suppressor. In contrast, in the MCF10CA1a cell line (M-IV), which gives rise to aggressive metastatic tumors, the tumor suppressor activity is lost and TGF-β promotes metastasis. To test the possible involvement of miRNAs in the TGF-β switch, we compared expression profiles of miRNAs by Next Gen miRNA sequencing 1) basally in cultures of all four cell lines and 2) in M-IIIcl4 and M-IV with and without TGF-β treatment. A variety of patterns of change in basal miRNA expression with malignant progression were seen. We focused on miRNAs whose expression level differs basally between M-IIIcl4 and M-IV, since the switch occurs between these two cell lines. 46 miRNAs were expressed &gt; 1.5 fold higher in M-IIIcl4 than in M-IV, whereas 29 miRNAs were expressed &gt; 1.5 fold higher in M-IV than in M-IIIcl4. We selected several miRNAs whose expression was most different between the two cell lines, and examined whether these miRNAs regulate cellular responses to TGF-β. As an example, let-7i and let-7g were expressed higher in M-IV than in M-IIIcl4. Forced expression of these miRNAs partially reversed TGF-β-induced growth inhibition in M-IIIcl4. A similar strategy was applied to miRNAs whose regulation by TGF-β is different between M-IIIcl4 and M-IV. The results of these experiments will be discussed.
Citation Format: Yoshiko Nagano, Maxwell P. Lee, Lalage M. Wakefield. Roles of miRNAs in the switch of TGF-β from tumor suppressor to pro-oncogenic factor in cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer; 2012 Jan 8-11; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(2 Suppl):Abstract nr A7.