Making Science Accessible: A Semiotics of Scientific Communication

This article serves as a demonstration of how certain models of literary analysis, used to theorize and analyze fiction and narrative, can also be applied to scientific communication in such a manner as to promote the accessibility of science to the general public and a greater awareness of the methodology used in making scientific discovery. The approach of this article is based on the assumption that the principles of structuralism and semiotics can provide plausible explanations for the divide between the reception of science and literature. We provide a semiotic analysis of a scientific article that has had significant impact in the field of molecular biology with profound medical implications. Furthermore, we show how the structural and semiotic characteristics of literary texts are also evident in the scientific papers, and we address how these characteristics can be applied to scientific prose in order to propose a model of scientific communication that reaches the public. By applying this theoretical framework to the analysis of both scientific and literary communication, we establish parallels between primary scientific texts and literary prose.     

CLIP-170S is a microtubule +TIP variant that confers resistance to taxanes by impairing drug-target engagement

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A rapid assay for drug sensitivity of glioblastoma stem cells

Glioblastoma (GBM) is a highly infiltrating, aggressive brain cancer with no available curative treatment. We developed a rapid assay for assessing the effect of various drugs on GBM stem cells. The assay uses a small number of separated CD133+ cells (20,000 in 0.2 ml) in 96-well plate that form neurospheres within 1-2 days. Various drugs disperse the neurospheres within 24-36 h, which can be quantified microscopically. We used the GBM cell line A-172 to develop the conditions for the assay, utilizing Gleevec, the gamma-secretase inhibitor DAPT, and the anti-bacterial peptide amph1D. The results show dispersion of the neurospheres leading to cell death, at relatively low drugs concentrations (<25 microM). Drug combination showed a synergistic effect and disruption of neurospheres under lower concentrations. We applied this assay to the CD133+ cells of surgical specimens from three patients that showed similar results. This assay facilitates a rapid test of drugs on small amounts of fractionated patient's GBM stem cells.     

A PDE Model for Imatinib-Treated Chronic Myelogenous Leukemia

We derive a model for describing the dynamics of imatinib-treated chronic myelogenous leukemia (CML). This model is a continuous extension of the agent-based CML model of Roeder et al. (Nat. Med. 12(10), 1181–1184, 2006) and of its recent formulation as a system of difference equations (Kim et al. in Bull. Math. Biol. 70(3), 728–744, 2008). The new model is formulated as a system of partial differential equations that describe various stages of differentiation and maturation of normal hematopoietic cells and of leukemic cells. An imatinib treatment is also incorporated into the model. The simulations of the new PDE model are shown to qualitatively agree with the results that were obtained with the discrete-time (difference equation and agent-based) models. At the same time, for a quantitative agreement, it is necessary to adjust the values of certain parameters, such as the rates of imatinib-induced inhibition and degradation.     

Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex

We report a clustering of public human protein kinase structures based on the conformations of two structural elements, the activation segment and the C-helix, revealing three discrete clusters. One cluster includes kinases in catalytically active conformations. Each of the other clusters contains a distinct inactive conformation. Typically, kinases adopt at most one of the inactive conformations in available X-ray structures, implying that one of the conformations is preferred for many kinases. The classification is consistent with selectivity profiles of several well-characterized kinase inhibitors. We show further that inhibitor selectivity profiles guide kinase classification. For example, selective inhibition of lck among src-family kinases by imatinib (Gleevec) suggests that the relative stabilities of inactive conformations of lck are different from other src-family kinases. We report the X-ray structure of the lck/imatinib complex, confirming that the conformation adopted by lck is distinct from other structurally-characterized src-family kinases and instead resembles kinases abl1 and kit in complex with imatinib. Our classification creates new paths for designing small-molecule inhibitors.     

格列卫与多西紫杉醇联合对人乳腺癌细胞株MCF-7及其裸鼠移植瘤的作用

目的：探讨分子靶向药物格列卫与多西紫杉醇联合对人乳腺癌细胞株MCF-7的凋亡及其裸鼠皮下移植瘤生长的影响。方法：采用流式细胞检测仪检测MCF-7细胞在格列卫与多西紫杉醇单独处理及共同处理条件下的凋亡率;建立人乳腺癌细胞株MCF-7裸鼠皮下移植瘤模型,观察格列卫与多西紫杉醇单独治疗组及联合治疗组移植瘤的生长,计算抑瘤率。结果：MCF-7细胞在格列卫与多西紫杉醇共同处理条件下的凋亡率（50.86%）远高于多西紫杉醇单独处理（22.06%）及同剂量格列卫组单独处理（8.13%）条件下的凋亡率;高剂量多西紫杉醇与格列卫联合组肿瘤质量与单独多西紫杉醇组比较,差异虽然没有显著性,但联合组抑瘤率高达99.55%,高于多西紫杉醇组（97.43%）,q值为1.014;中剂量多西紫杉醇与格列卫联合组肿瘤质量与单独多西紫杉醇组比较,差异有高度显著性,联合组抑瘤率达96.53%,高于多西紫杉醇组（92.01%）,q值为1.02;低剂量多西紫杉醇与格列卫联合组肿瘤质量与单独多西紫杉醇组比较,差异有高度显著性,联合组抑瘤率达68.20%,高于多西紫杉醇组（58.40%）,q值为1.004。结论：格列卫与凋亡诱导剂多西紫杉醇共同处理MCF—7细胞能达到协同诱导凋亡的效果;高、中、低剂量的多西紫杉醇与格列卫联合对人乳腺癌细胞株MCF-7裸鼠移植瘤增殖的抑制具有相加作用。     

The ErbB/HER receptor protein-tyrosine kinases and cancer

The ErbB/HER protein-tyrosine kinases, which include the epidermal growth factor receptor, consist of a growth-factor-binding ectodomain, a single transmembrane segment, an intracellular protein-tyrosine kinase catalytic domain, and a tyrosine-containing cytoplasmic tail. The genes for the four members of this family, ErbB1-ErbB4, are found on different human chromosomes. Null mutations of any of the ErbB family members result in embryonic lethality. ErbB1 and ErbB2 are overexpressed in a wide variety of tumors including breast, colorectal, ovarian, and non-small cell lung cancers. The structures of the ectodomains of the ErbB receptors in their active and inactive conformation have shed light on the mechanism of receptor activation. The extracellular component of the ErbB proteins consists of domains I-IV. The activating growth factor, which binds to domains I and III, selects and stabilizes a conformation that allows a dimerization arm to extend from domain II to interact with an ErbB dimer partner. As a result of dimerization, protein kinase activation, trans-autophosphorylation, and initiation of signaling occur. The conversion of the inactive to active receptor involves a major rotation of the ectodomain. The ErbB receptors are targets for anticancer drugs. Two strategies for blocking the action of these proteins include antibodies directed against the ectodomain and drugs that inhibit protein-tyrosine kinase activity. A reversible ATP competitive inhibitor of ErbB1 (ZD1839, or Iressa) and an ErbB1 ectodomain directed antibody (IMC-C225, or Erbitux) have been approved for the treatment of non-small cell lung cancer and colorectal cancer, respectively. An ErbB2/HER2 ectodomain directed antibody (trastuzumab, or Herceptin) has also been approved for the treatment of breast cancer. Current research promises to produce additional agents based upon these approaches.     

Regorafenib regresses an imatinib-resistant recurrent gastrointestinal stromal tumor (GIST) with a mutation in exons 11 and 17 of c-kit in a patient-derived orthotopic xenograft (PDOX) nude mouse model

Gastrointestinal stromal tumor (GIST) with a mutation in exons 11 and 17 of c-kit is a rare type of sarcoma. The aim of this study was to determine drug sensitivity for a regionally-recurrent case of GIST using a patient-derived orthotopic xenograft (PDOX) model. The PDOX model was established in the anterior wall of the stomach. GIST PDOX models were randomized into 5 groups of 6 mice each when the tumor volume reached 60 mm³: G1, control group; G2, imatinib group (oral administration (p.o.), daily, for 3 weeks); G3, sunitinib group (p.o., daily, for 3 weeks); G4, regorafenib (p.o., daily, for 3 weeks); G5, pazopanib (p.o., daily, for 3 weeks). All mice were sacrificed on day 22. Tumor volume was evaluated on day 0 and day 22 by laparotomy. Body weight were measured 2 times per week. Though regorafenib is third-line therapy for GIST, it was the most effective drug and regressed the tumor significantly (p < 0.001). Sunitinib suppressed tumor growth compared to the control group (p = 0.002). Imatinib, first-line therapy for GIST, and pazopanib did not have significant efficacy compared to the control group (p = 0.886, p = 0.766). The implications of this result is discussed for GIST patients.     

Modeling Imatinib-Treated Chronic Myelogenous Leukemia: Reducing the Complexity of Agent-Based Models

We develop a model for describing the dynamics of imatinib-treated chronic myelogenous leukemia. Our model is based on replacing the recent agent-based model of Roeder et al. (Nat. Med. 12(10):1181–1184, 2006) by a system of deterministic difference equations. These difference equations describe the time-evolution of clusters of individual agents that are grouped by discretizing the state space. Hence, unlike standard agent-base models, the complexity of our model is independent of the number of agents, which allows to conduct simulation studies with a realistic number of cells. This approach also allows to directly evaluate the expected steady states of the system. The results of our numerical simulations show that our model replicates the averaged behavior of the original Roeder model with a significantly reduced computational cost. Our general approach can be used to simplify other similar agent-based models. In particular, due to the reduced computational complexity of our technique, one can use it to conduct sensitivity studies of the parameters in large agent-based systems.