Logical Development of the Cell Ontology

Background  

The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL.     

On the Segregation of the Germ and Somatic Cell Lines in the Embryo

Abstract. In this paper we argue that the mechanisms underlying the segregation of the somatic and germ cell lines are basically similar. The interaction of the genome with specific cytoplasmic factors is responsible for the restriction of their developmental potencies in the somatic cell lines, and for the prevention of such a restriction in the germ cell line. In particular, it is suggested that meiosis is part of the differentiation program of the germ cells.     

白细胞介素2受体在人各种肿瘤细胞表面的表达

鉴于白细胞介素2受体(IL-2R)在某些恶性骨髓瘤、白血病及异常的T、B细胞和单核细胞表面异常高表达,近年来对IL-2与IL-2R结合肽P1-30的研究不断深入。简要综述了近年来国内外报道的IL-2R及其各组分在多种肿瘤细胞表面的分布情况,为以IL-2R或其不同组分为靶标的靶向治疗药物研究提供理论依据。     

基于3-D图形表示的DNA序列的相似性分析

基于DNA序列的3D图形表示,通过L／L矩阵的规范化最大特征值组成的3维向量来刻画了DNA序列,并基于这种方法,用β-globin基因的第一个外显子分析了11个物种的相似性问题。     

Development of New Cell Lines for Animal Cell Biotechnology

Abstract

Mammalian cell culture has been an important technique in laboratory-scale experimentation for many decades. Developments in large-scale culture have been due to the need to grow large numbers of cells to support the growth of viruses for vaccine production, and more recently, for growing hybridoma cells as a source of monoclonal antibody. Increasingly, however, pharmaceutical products such as hormones, enzymes, growth factors, and clotting factors are being produced from cell lines which have been manipulated by recombinant DNA techniques. It is clear, therefore, that the high cost of growing mammalian cells on a large scale does not necessarily prohibit their use for biotechnology, and indeed there is considerable evidence to suggest that animal cell biotechnology will continue to be a major growth area in the future.     

Glial Cell Lines: An Overview

The importance and essential functions of glial cells in the nervous system are now beginning to be understood and appreciated. Glial cell lines have been instrumental in the elucidation of many of these properties. In this Overview, the origin and properties of most of the existing cell lines for the major glial types: oligodendroglia, astroglia, microglia and Schwann cells, are documented. Particular emphasis is given to the culture conditions for each cell line and the degree to which the line can differentiate in vitro and in vivo. The major molecular markers for each glial cell lines are indicated. Finally, methods by which the glial cell lines have been developed are noted and the future directions of glial cell line research are discussed.     

Ion Channel Phenotype of Melanoma Cell Lines

Melanoma cells are transformed melanocytes of neural crest origin. K⁺ channel blockers have been reported to inhibit melanoma cell proliferation. We used whole-cell recording to characterize ion channels in four different human melanoma cell lines (C8161, C832C, C8146, and SK28). Protocols were used to identify voltage-gated (K_V), Ca²⁺-activated (K_Ca), and inwardly rectifying (K_IR) K⁺ channels; swelling-sensitive Cl⁻ channels (Cl_swell); voltage-gated Ca²⁺ channels (Ca_V) and Ca²⁺ channels activated by depletion of intracellular Ca²⁺ stores (CRAC); and voltage-gated Na⁺ channels (Na_V). The presence of Ca²⁺ channels activated by intracellular store depletion was further tested using thapsigargin to elicit a rise in [Ca²⁺] _i . The expression of K⁺ channels varied widely between different cell lines and was also influenced by culture conditions. K_IR channels were found in all cell lines, but with varying abundance. Whole-cell conductance levels for K_IR differed between C8161 (100 pS/pF) and SK28 (360 pS/pF). K_Ca channels in C8161 cells were blocked by 10 nm apamin, but were unaffected by charybdotoxin (CTX). K_Ca channels in C8146 and SK28 cells were sensitive to CTX (K _d = 4 nm), but were unaffected by apamin. K_V channels, found only in C8146 cells, activated at ∼−20 mV and showed use dependence. All melanoma lines tested expressed CRAC channels and a novel Cl_swell channel. Cl_swell current developed at 30 pS/sec when the cells were bathed in 80% Ringer solution, and was strongly outwardly rectifying (4:1 in symmetrical Cl⁻). We conclude that different melanoma cell lines express a diversity of ion channel types. Received: 2 April 1996/Revised: 22 August 1996     

Fish Hereditary Melanoma Cell Lines of Different Degrees of Cell Differentiation

Four cell lines including two sublines were established from hereditary melanomas in interspecific hybrids between platyfish ( Xiphophorus maculatus ) carrying the Sp gene and swordtails ( X. helleri ) and maintained in vitro for more than 34 months. Cells in each cell line grew randomly across each other with an apparent lack of contact inhibition of growth and at a population doubling time of 50 to 72 hr. They retained the characteristics of young pigment cells in regard to ultrastructure, tyrosinase activity, the DOPA and combined DOPA-premelanin reactions. In the degree of differentiation, the cells of the three cell lines seemed comparable to early melanocytes close to melanoblasts, and those of the remaining one cell line seemed comparable to young melanocytes but were in a more differentiated state than the early melanocytes. Colony forming ability on plastic plates was at a level of 10% in the three cell lines but only 1% in the one cell line. All four cell lines failed to form colonies in soft agar. Chromosome analysis revealed that these four cell lines were heteroploid with many abnormal figures of chromosomes and double minute chromosomes. None of the cell lines showed transplantability to fish.     

Mathematical Determination of Cell Population Doubling Times for Multiple Cell Lines

Cell cycle times are vital parameters in cancer research, and short cell cycle times are often related to poor survival of cancer patients. A method for experimental estimation of cell cycle times, or doubling times of cultured cancer cell populations, based on addition of paclitaxel (an inhibitor of cell division) has been proposed in literature. We use a mathematical model to investigate relationships between essential parameters of the cell division cycle following inhibition of cell division. The reduction in the number of cells engaged in DNA replication reaches a plateau as the concentration of paclitaxel is increased; this can be determined experimentally. From our model we have derived a plateau log reduction formula for proliferating cells and established that there are linear relationships between the plateau log reduction values and the reciprocal of doubling times (i.e. growth rates of the populations). We have therefore provided theoretical justification of an important experimental technique to determine cell doubling times. Furthermore, we have applied Monte Carlo experiments to justify the suggested linear relationships used to estimate doubling time from 5-day cell culture assays. We show that our results are applicable to cancer cell populations with cell loss present.     

Characterization of Kanamycin-Resistant Cell Lines of Nicotiana tabacum

Two kanamycin-resistant variants of Nicotiana tabacum were derived by culturing seedling leaf sections on a shoot-inducing medium containing kanamycin. The variants displayed a higher resistance to the structurally related antibiotic streptomycin than to kanamycin. The resistance phenotype was expressed when the tissue was cultured either as callus or as a differentiating tissue and was stably maintained in the absence of kanamycin. Plants regenerated from the variant lines had morphologically abnormal flowers and produced few viable seeds. These resistant lines are potentially useful for protoplast fusion or genetic modification experiments requiring selectable phenotypic markers.     

Retinoids Differentially Regulate the Proliferation of Colon Cancer Cell Lines

In this study, the proliferative effects of retinoids were examined in the MC-26 and LoVo colon adenocarcinoma cell lines. The proliferation of the LoVo cell line was not altered in the presence of the retinoidsall trans-retinoic acid (atRA) and 9-cis-retinoic acid (9-cis-RA). Both retinoids, however, stimulated the growth, as measured by cell proliferation, of MC-26 cells.atRA and 9-cis-RA were equipotent in increasing MC-26 cell proliferation, suggesting that the growth stimulation is mediated by one or more retinoic acid receptors (RARs). To determine the RAR which might be responsible for this growth stimulatory effect, we characterized the RAR subtypes which were present in both cell lines. mRNA for the RARα, RARβ, and RARγ were detected in the MC-26 cell. Of the RARs present in MC-26 cells, the RARα does not mediate the growth stimulatory effects of retinoids, for a selective RARα antagonist was unable to prevent the retinoid-induced increase in MC-26 cell growth. RARα, RARβ, and RARγ mRNA are also expressed in the LoVo cell line; the lack of growth-stimulation by retinoids in LoVo cells, therefore, does not seem to be due to the absence of RARs. The results obtained in these experiments demonstrate that the growth response elicited by retinoids can vary between colon cancer cells and that the differences in response may not be solely determined by the RAR subtypes which are expressed in a colon cancer cell line.     

Differential SELEX in Human Glioma Cell Lines

The hope of success of therapeutic interventions largely relies on the possibility to distinguish between even close tumor types with high accuracy. Indeed, in the last ten years a major challenge to predict the responsiveness to a given therapeutic plan has been the identification of tumor specific signatures, with the aim to reduce the frequency of unwanted side effects on oncologic patients not responding to therapy. Here, we developed an in vitro evolution-based approach, named differential whole cell SELEX, to generate a panel of high affinity nucleic acid ligands for cell surface epitopes. The ligands, named aptamers, were obtained through the iterative evolution of a random pool of sequences using as target human U87MG glioma cells. The selection was designed so as to distinguish U87MG from the less malignant cell line T98G. We isolated molecules that generate unique binding patterns sufficient to unequivocally identify any of the tested human glioma cell lines analyzed and to distinguish high from low or non-tumorigenic cell lines. Five of such aptamers act as inhibitors of specific intracellular pathways thus indicating that the putative target might be important surface signaling molecules. Differential whole cell SELEX reveals an exciting strategy widely applicable to cancer cells that permits generation of highly specific ligands for cancer biomarkers.     

Aphid-Symbiotic Bacteria Cultured in Insect Cell Lines

The cells and tissues of many aphids contain bacteria known as “secondary symbionts,” which under specific environmental circumstances may be beneficial to the host insect. Such symbiotic bacteria are traditionally described as intractable to cultivation in vitro. Here we show that two types of aphid secondary symbionts, known informally as T type and U type, can be cultured and maintained in three insect cell lines. The identities of the cultured bacteria were confirmed by PCR with sequencing of 16S rRNA gene fragments and fluorescence in situ hybridization. In cell lines infected with bacteria derived from aphids harboring both T type and U type, the U type persisted, while the T type was lost. We suggest that the two bacteria persist in aphids because competition between them is limited by differences in tropism for insect tissues or cell types. The culture of these bacteria in insect cell lines provides a new and unique research opportunity, offering a source of unibacterial material for genomic studies and a model system to investigate the interactions between animal cells and bacteria. We propose the provisional taxon names “Candidatus Consessoris aphidicola” for T type and “Candidatus Adiaceo aphidicola” for U type.     

Establishment of Epstein-Barr Virus Growth-transformed Lymphoblastoid Cell Lines

Infection of B cells with Epstein-Barr virus (EBV) leads to proliferation and subsequent immortalization, resulting in establishment of lymphoblastoid cell lines (LCL) in vitro. Since LCL are latently infected with EBV, they provide a model system to investigate EBV latency and virus-driven B cell proliferation and tumorigenesis¹. LCL have been used to present antigens in a variety of immunologic assays^{2, 3}. In addition, LCL can be used to generate human monoclonal antibodies^{4, 5} and provide a potentially unlimited source when access to primary biologic materials is limited^{6, 7}.A variety of methods have been described to generate LCL. Earlier methods have included the use of mitogens such as phytohemagglutinin, lipopolysaccharide⁸, and pokeweed mitogen⁹ to increase the efficiency of EBV-mediated immortalization. More recently, others have used immunosuppressive agents such as cyclosporin A to inhibit T cell-mediated killing of infected B cells^{7, 10-12}.The considerable length of time from EBV infection to establishment of cell lines drives the requirement for quicker and more reliable methods for EBV-driven B cell growth transformation. Using a combination of high titer EBV and an immunosuppressive agent, we are able to consistently infect, transform, and generate LCL from B cells in peripheral blood. This method uses a small amount of peripheral blood mononuclear cells that are infected in vitroclusters of cells can be demonstrated. The presence of CD23 with EBV in the presence of FK506, a T cell immunosuppressant. Traditionally, outgrowth of proliferating B cells is monitored by visualization of microscopic clusters of cells about a week after infection with EBV. Clumps of LCL can be seen by the naked eye after several weeks. We describe an assay to determine early if EBV-mediated growth transformation is successful even before microscopic clusters of cells can be demonstrated. The presence of CD23^hiCD58⁺ cells observed as early as three days post-infection indicates a successful outcome.