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.     

A Maturity-Time Representation for Cell Populations

A maturity-time representation for the study of cell populations is introduced, which differs from the age-time representation suggested by von Foerster. A significant feature of the theory is the concept of maturation velocity. A solution to the fundamental equations of the theory is presented in terms of the individual generations which make up the population at any time. The problem of variability of generation time is considered from the differing viewpoints of the two representations, as well as that of an alternate theory due to Stuart and Merkle. The experimental observations of Prescott concerning the generation time distribution and population growth of Tetrahymena geleii HS cells appear to support best the theoretical formulation of the maturity-time representation. In particular, they suggest that memory of the maturation velocity or generation time of a given cell tends to persist from parent to daughter for several generations at least.     

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement

Accurate identification of cell types from single-cell RNA sequencing(scRNA-seq) data plays a critical role in a variety of scRNA-seq analysis studies. This task corresponds to solving an unsupervised clustering problem, in which the similarity measurement between cells affects the result significantly. Although many approaches for cell type identification have been proposed,the accuracy still needs to be improved. In this study, we proposed a novel single-cell clustering framework based on similarity learning, called SSRE. SSRE models the relationships between cells based on subspace assumption, and generates a sparse representation of the cell-to-cell similarity.The sparse representation retains the most similar neighbors for each cell. Besides, three classical pairwise similarities are incorporated with a gene selection and enhancement strategy to further improve the effectiveness of SSRE. Tested on ten real scRNA-seq datasets and five simulated datasets, SSRE achieved the superior performance in most cases compared to several state-of-the-art single-cell clustering methods. In addition, SSRE can be extended to visualization of scRNA-seq data and identification of differentially expressed genes. The matlab and python implementations of SSRE are available at https://github.com/CSUBioGroup/SSRE.     

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.     

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.     

永生化后细胞的生物学特性

近年来,永生化细胞技术快速发展,对细胞生物学特性的研究及其临床应用具有深远的意义。目前通过导入永生化基因SV40抗原和hTERT基因成为细胞永生化的常用方法,但存在安全性隐患。利用可逆性永生化技术,使细胞在获得永生化能力的同时去除永生化基因,使细胞恢复到原始状态。文章综述了永生化后细胞生物学特性的变化,并讨论了临床应用可能面临的问题。     

Growth of Fish Cell Lines on Microcarriers

Microcarrier beads were evaluated as substrates for the propagation of five anchorage-dependent fish cell lines. Growth of rainbow trout gonad (RTG-2) and Atlantic salmon cells was limited on microcarriers maintained in suspension. However, stationary microcarriers were suitable substrates for the growth of RTG-2, AS, Chinook salmon embryo (CHSE-214), and fathead minnow cells. Cell yields ranged from 2 × 10⁶ to 2.9 × 10⁶ cells per ml, representing 7- to 10-fold increases over the initial cell concentrations. The yield of new RTG-2 cells per unit volume of growth medium was 2.8 times greater in microcarrier cultures than in standard monolayer cultures. Northern pike cells failed to grow on microcarriers. Yields of infectious pancreatic necrosis virus propagated in microcarrier cultures of RTG-2 cells were more than twice the yields in standard monolayer cultures. The greater economy of microcarrier cultures in terms of growth vessel and medium requirements holds great promise for the large-scale production of anchorage-dependent fish cell cultures and fish viruses.     

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     

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.     

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.     

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.