Persistently elevated frequency of spontaneous mutations in progeny of CHO clones surviving X-irradiation: association with delayed reproductive death phenotype

Certain clonal progeny of Chinese hamster ovary (CHO) cells surviving X-irradiation demonstrate pleomorphic changes including a persistently decreased cloning efficiency, a dominant phenotype we have termed delayed reproductive death (Chang and Little, 1991, 1992b). We now report that cells from these progeny clones show a persistently elevated frequency of spontaneous mutations at the hprt locus for up to 95–100 population doubling post-irradiation. Mutant fractions as high as 10⁻³ were scored, more than two orders of magnitude higher than those observed in clonal progeny of non-irradiated cells studied in parallel. These results are discussed in terms of the hypothesis that radiation induces a type of genetic instability among some surviving cells that results in a heritable mutator phenotype, and that this instability may also be involved in the phenomenon of delayed reproductive death.     

Sex differences in optimal incubation temperatures in a scincid lizard species

Most theoretical models for the evolution of temperature-dependent sex determination (TSD) rely upon differential fitness of male and female offspring incubated under different thermal regimes. However, there are few convincing data on this topic. We studied incubation effects in a lizard species (Bassiana duperreyi, Scincidae) with genotypic sex determination, so that we could separate effects due to incubation temperatures from those due to offspring gender. We incubated eggs under two different fluctuating-temperature regimes that simulated hot and cold natural nest-sites. The effects of our incubation treatments on phenotypes of the hatchling lizards (morphology and locomotor performance) differed between the sexes. Females emerging from eggs exposed to the “hot nest” treatment (diel cycling, 23–31°C) were larger, and ran faster, than did their sisters from the “cold nest” treatment (16–24°C). Males showed a smaller and less consistent phenotypic response than females. These incubation-induced responses were relatively stable during the first few weeks of life post-hatching, at least in captive lizards maintained under laboratory conditions. These kinds of sex differences in the phenotypic responses of hatchling reptiles to incubation conditions provide a plausible basis for the evolution of temperature-dependent sex determination in reptiles. Received: 07 May 1998 / Accepted: 16 November 1998     

Induction and specification of midbrain dopaminergic cells: focus on SHH,FGF8, and TGF-β

Cell-fate decisions along the dorsoventral and anterior–posterior axis of the neural tube are dictated by factors from signaling and organizing centers. According to the prevailing notion, the formation of mesencephalic dopaminergic neurons is directed by diffusable signals from the notochord, floor plate, and isthmic organizer. Sonic hedgehog (Shh), secreted by the notochord and floor plate, and fibroblast growth factor (FGF) 8, secreted by the isthmus, are thought to be key molecules involved in the development of midbrain dopaminergic neurons. During the last decade, the introduction of elegant explant culture systems and the generation of transgenic and mutant mice have greatly contributed to a better understanding of the molecular signals that direct the induction and specification of midbrain dopaminergic neurons. In this context, experimental evidence has challenged the dominant roles of Shh and FGF8 in dopaminergic neuron development. Additional molecules have been identified as being required for the generation of mesencephalic dopaminergic neurons, particularly members of the transforming growth factor beta superfamily. The work carried out in the authors laboratories was supported by grants from the Deutsche Forschungsgemeinschaft     

Genomics refutes an exclusively African origin of humans

Ten years ago, evidence from genetics gave strong support to the "recent African origin" view of the evolution of modern humans, which posits that Homo sapiens arose as a new species in Africa and subsequently spread, leading to the extinction of other archaic human species. Subsequent data from the nuclear genome not only fail to support this model, they do not support any simple model of human demographic history. In this paper, we study a process in which the modern human phenotype originates in Africa and then advances across the world by local demic diffusion, hybridization, and natural selection. While the multiregional model of human origins posits a number of independent single locus selective sweeps, and the "out of Africa" model posits a sweep of a new species, we study the intermediate case of a phenotypic sweep. Numerical simulations of this process replicate many of the seemingly contradictory features of the genetic data, and suggest that as much as 80% of nuclear loci have assimilated genetic material from non-African archaic humans.     

Phenotypic and genotypic characterization of mutants of the virginiamycin producing strain 899 and its relatedness to the type strain of Streptomyces virginiae

A representative set of 19 mutants, with a known genealogy, of the virginiamycin producing strain Streptomyces virginiae 899 was investigated phenotypically and genotypically. Colour of the aerial and substrate mycelium were very variable both among spontaneous variants and those obtained after induced mutagenesis. At genotypic level, all mutants showed nearly identical BOX patterns, not reflecting the phenotypic heterogeneity observed. More than 40 years of forced mutational pressure did not cause huge chromosomal distortions but was most likely limited to base substitutions. The species S. virginiae, including besides producers of virginiamycin the type strain and non-type strains producing other bioactive compounds, is genomically heterogeneous on the basis of BOX-PCR fingerprinting and DNA-DNA hybridizations. The virginiamycin producing strain 899 does not belong to the species S. virginiae despite its phenotypic similarity to the latter.     

Genes involved in phenotypic and antigenic variation in African trypanosomes and malaria

Large polymorphic gene families that are involved in clonal phenotypic variation have been identified in both African trypanosomes and malaria parasites. Many of these gene families are necessary for host adaptation, allowing the parasite to infect different species of host or types of host cells. In many cases, switching between these functionally variable proteins also results in antigenic variation.     

Rapid Analysis and Exploration of Fluorescence Microscopy Images

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized image analysis tools are available, most traditional image-analysis-based workflows have steep learning curves (for fine tuning of analysis parameters) and result in long turnaround times between imaging and analysis. In particular, cell segmentation, the process of identifying individual cells in an image, is a major bottleneck in this regard.Here we present an alternate, cell-segmentation-free workflow based on PhenoRipper, an open-source software platform designed for the rapid analysis and exploration of microscopy images. The pipeline presented here is optimized for immunofluorescence microscopy images of cell cultures and requires minimal user intervention. Within half an hour, PhenoRipper can analyze data from a typical 96-well experiment and generate image profiles. Users can then visually explore their data, perform quality control on their experiment, ensure response to perturbations and check reproducibility of replicates. This facilitates a rapid feedback cycle between analysis and experiment, which is crucial during assay optimization. This protocol is useful not just as a first pass analysis for quality control, but also may be used as an end-to-end solution, especially for screening. The workflow described here scales to large data sets such as those generated by high-throughput screens, and has been shown to group experimental conditions by phenotype accurately over a wide range of biological systems. The PhenoBrowser interface provides an intuitive framework to explore the phenotypic space and relate image properties to biological annotations. Taken together, the protocol described here will lower the barriers to adopting quantitative analysis of image based screens.     

Phenotypic Variation and Systemic Cancer in the FAMMM Syndrome

Familial atypical multiple mole melanoma (FAMMM) syndrome, a cancer-associated genodermatosis, is a dominantly inherited heterogeneous disorder with variable expressivity of both its cutaneous and cancer phenotypes. By using a verified historical review technique of cancer documentation (idout patient health records, pathology reports/slides, autopsy reports/slides, and death certificates) of all anatomic sites in all members of a modified nuclear pedigree (first-degree relatives plus maternal and paternal grandparents, aunts, and uncles) over several generations, we showed that the FAMMM syndrome is similar to the majority of autosomal dominant inherited cancer-associated genodermatoses and has excessive risk for cancer of multiple anatomic sites. With respect to the FAMMM syndrome, these cancers involved the breast, respiratory tract, gastrointestinal system, the eye (intraocular melanoma), and the lymphatic system. These FAMMM pedigrees showed some of the following distinctive characteristics of hereditary cancer: 1) integral patterns of cancer within and between pedigrees; 2) early age of onset of cancer; 3) prolonged survival of some pedigree members with cancer; and 4) an excess of multiple primary melanomas and cancers of variable anatomic sites. The presence of these features indicates that these cancers of variable anatomic sites may be etiologically associated with the FAMMM syndrome. Heterogeneity should be investigated in FAMMM pedigrees with attention to consistent differences in size and distribution of atypical lesions, age at cancer onset, and pattern of tumor occurrences. The occurrence of FAMMM pedigrees in the general population or among pedigrees of probands with atypical nevi is not known. The occurrence of systemic cancers in these FAMMM pedigrees requires the development of cancer surveillance programs that are specifically modified to the particular cancer pattern of each pedigree.     

Simulations in Evolution. III. Randomness as a Generator of Opportunities

In Neo‐Darwinism, variation and natural selection are the two evolutionary mechanisms which propel biological evolution. Our previous reports presented a histogram model to simulate the evolution of populations of individuals classified into bins according to an unspecified, quantifiable phenotypic character, and whose number in each bin changed generation after generation under the influence of fitness, while the total population was maintained constant. The histogram model also allowed Shannon entropy (SE) to be monitored continuously as the information content of the total population decreased or increased. Here, a simple Perl (Practical Extraction and Reporting Language) application was developed to carry out these computations, with the critical feature of an added random factor in the percent of individuals whose offspring moved to a vicinal bin. The results of the simulations demonstrate that the random factor mimicking variation increased considerably the range of values covered by Shannon entropy, especially when the percentage of changed offspring was high. This increase in information content is interpreted as facilitated adaptability of the population.     

MDMPR:小鼠发育代谢表型库

小鼠发育代谢表型库(Mouse Developmental and Metabolic Phenotype Repository,MDMPR)是一个致力于小鼠资源和表型数据实时共享的开放性平台,它依托于科技部重点研发计划“发育编程及其代谢调节”专项项目“建立小鼠发育代谢表型库”。该项目预计在5年内完成500个发育代谢相关小鼠敲除模型的建立,并对其表型数据进行标准化的解析、建立表型数据库。MDMPR作为一个资源及数据集成的库,由多个子系统作为支撑,包括ES细胞数据库、项目管理系统、繁育管理系统、精子库管理系统、表型分析系统,信息化管理深入到项目中每个环节,从基因突变ES细胞制备、基因突变小鼠制备、小鼠繁育,精子冻存到最终的表型分析、数据处理及展示,保证了MDMPR产生数据的真实性及实时性。MDMPR除了不断地推进项目进行,增加自身产生的数据外,也在积极的整合其他的资源及数据,如人特异性基因敲除ES细胞库、蛋白相互作用数据库(STRING)、核心转录调节环路(dbCoRc)和Enhancer-Indel数据库,今后还将进一步整合,帮助发育代谢及其他领域的研究人员能够一站式的获取所需资源和数据、加快研究进程,最终服务于全人类的医疗事业。