Introduction: Patterns of generational change: convergent,reactive or emergent?

Abstract

The aim of this special issue is to map the extent of generational change among Britain's ethnic minority population and to understand some of the underlying processes involved. Is there greater integration across generations, or has the ‘new second generation’ in Britain remained isolated from the mainstream, perhaps as a result of the prejudice and discrimination from the white British that they have encountered or because of desires to maintain ethnic values and resist western practices? We also ask whether processes of generational change have proceeded at the same pace and direction in different domains – notably cultural, social, structural and political – and whether it has proceeded at the same pace among different minorities.     

枯草芽孢杆菌整合载体研究进展

芽孢杆菌质粒经常在复制时出现不稳定的单链(ssDNA)形式,从而导致质粒载体的丢失,而采用整合载体将克隆基因整合到宿主染色体,是克服枯草杆菌质粒不稳定性的一个有效途径。本综述了芽孢杆菌整合载体的研究历程、整合机理、整合类型及其应用和前景。     

A highly efficient single-step,markerless strategy for multi-copy chromosomal integration of large biochemical pathways in Saccharomyces cerevisiae

Despite recent advances in genome editing capabilities for the model organism Saccharomyces cerevisiae, the chromosomal integration of large biochemical pathways for stable industrial production remains challenging. In this work, we developed a simple platform for high-efficiency, single-step, markerless, multi-copy chromosomal integration of full biochemical pathways in Saccharomyces cerevisiae. In this Di-CRISPR (delta integration CRISPR-Cas) platform based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated systems (Cas), we specifically designed guide RNA sequences to target multiple delta sites in the yeast genome. The generation of double stranded breaks at the delta sites allowed simultaneous integration of multiple copies of linearized donor DNA containing large biochemical pathways. With our newly developed Di-CRISPR platform, we were able to attain highly efficient and markerless integration of large biochemical pathways and achieve an unprecedented 18-copy genomic integration of a 24 kb combined xylose utilization and (R,R)-2,3-butanediol (BDO) production pathway in a single step, thus generating a strain that was able to produce BDO directly from xylose. The simplicity and high efficiency of the Di-CRISPR platform could provide a superior alternative to high copy plasmids and would render this platform an invaluable tool for genome editing and metabolic engineering in S. cerevisiae.     

Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes

Bornaviruses are the only animal RNA viruses that establish a persistent infection in their host cell nucleus. Studies of bornaviruses have provided unique information about viral replication strategies and virus–host interactions. Although bornaviruses do not integrate into the host genome during their replication cycle, we and others have recently reported that there are DNA sequences derived from the mRNAs of ancient bornaviruses in the genomes of vertebrates, including humans, and these have been designated endogenous borna-like (EBL) elements. Therefore, bornaviruses have been interacting with their hosts as driving forces in the evolution of host genomes in a previously unexpected way. Studies of EBL elements have provided new models for virology, evolutionary biology and general cell biology. In this review, we summarize the data on EBL elements including what we have newly identified in eukaryotes genomes, and discuss the biological significance of EBL elements, with a focus on EBL nucleoprotein elements in mammalian genomes. Surprisingly, EBL elements were detected in the genomes of invertebrates, suggesting that the host range of bornaviruses may be much wider than previously thought. We also review our new data on non-retroviral integration of Borna disease virus.     

Creating Science Picture Books for an Authentic Audience

This article presents an authentic writing opportunity to help ninth-grade students use the writing process in a science classroom to write and illustrate picture books for fourth-grade students to demonstrate and share their understanding of a biology unit on cells. By creating a picture book, students experience the writing process, understand how to share their learning with an authentic audience, and create an artifact that demonstrates their understanding of content knowledge.     

T-DNA整合的研究进展

根癌农杆菌介导的基因转化过程中,T-DNA的整合是关系到外源基因能否稳定遗传的关键步骤。影响T-DNA整合的因素很多,包括毒性蛋白、寄主因子等等,本文对此加以综述,同时阐述了T-DNA在植物基因组中的整合及染色体水平上的分布及其整合模型。     

Morphometric analysis of the skull of Dermophis mexicanus (Amphibia: Gymnophiona)

The levels of integration, patterns of allometric growth and size-related differences in skull dimensions of the caecilian Dermophis mexicanus were investigated by means of univariate, bivariate and multivariate statistics. The analyses indicate that (1) most but not all measurements of the skull arc more variable in adults than in juveniles; (2) growth is allometric and results in changes in shape between juveniles and adults; (3) there is a high level of integration of all variables by general size; and (4) homologous paired measurements show concordant allometric trends and are integrated beyond the sole effect of general size. These analyses provide baseline data, a set of hypotheses and a methodological framework for comparative studies of patterns of variation and integration among caecilians and among other vertebrates.     

Molecular analysis of transgene and vector backbone integration into the barley genome following Agrobacterium-mediated transformation

We report a large-scale study on the frequency of transgene and T-DNA backbone integration following Agrobacterium-mediated transformation of immature barley embryos. One hundred and ninety-one plant lines were regenerated after hygromycin selection and visual selection for GFP expression at the callus stage. Southern blotting performed on a subset of 53 lines that were PCR positive for the GFP gene documented the integration of the GFP gene in 27 of the lines. Twenty-three of these lines expressed GFP in T₁ plantlets. Southern blotting with a vector backbone probe revealed that 13 of the 27 lines possessed one or more vector backbone fragments illustrating the regular occurrence of vector backbone integration following Agrobacterium infection of barley immature embryos.     

重组腺相关病毒载体的整合性研究进展

重组腺相关病毒(rAAV)载体是一种具有高靶向性和良好安全性的病毒载体,在基因治疗中得到了较为广泛的应用。目前全球范围内已有70余项以rAAV为基因药物的临床研究已经完成或正在进行中。与野生型AAV(wtAAV)定点整合不同,不表达Rep蛋白的rAAV载体与宿主染色体发生的是随机整合,而这给临床应用带来了可能的潜在的安全隐患。该文在综述wtAAV和rAAV整合机理的基础上对rAAV的因随机整合而可能导致的致癌性及其他后果进行探讨,并总结了相应应对策略,特别是目前利用Rep蛋白所开展的定点整合研究。     

Turning pipe dreams into reality

ABSTRACT: A report on the Galaxy Community Conference at the University of Illinois, Chicago, July 25-27, 2012.     

Random transposon vectors pUTTns for the markerless integration of exogenous genes into gram-negative eubacteria chromosomes

A set of random transposon vectors pUTTns that facilitates the markerless integration of new functions into the chromosome of gram-negative bacteria has been developed. The vectors, which are derived from mini-Tn5 transposons, are located on a R6K-based suicide delivery plasmid that provides the IS50_R transposase tnp gene in cis, but they are external to the mobile element. The vectors' conjugal transfer to recipients is mediated by RP4 mobilization functions in the donor. Internal to the mini-Tn5 element is a cassette that contains a selectable antibiotic resistance marker (kanamycin, chloramphenicol, or tetracycline resistance gene), a counter-selectable marker (sacB), a 430-bp repeat of the sacB gene 3′ end acted as the directly-repeated (DR) sequence, and modified multiple cloning sites (MCS). After two total rounds of transposon integration and recombination between the two DRs, only the exogenous DNA inserted into the MCS (passenger genes) and a single 430-bp scar sacBDR fragment remained in the chromosome after excision. The utility of these vectors was demonstrated by integrating the organophosphorus insecticide hydrolase gene (mpd) into the chromosome of Escherichia, Pseudomonas, Sphingomonas, and Paracoccus species. Sequential integration of another organophosphorus insecticide hydrolase gene (oph) into the previously engineered bacteria, without bringing any selectable markers, was also successful. These engineered bacteria were relatively stable. Cell viability and original degrading characteristics were not affected compared with the original recipients. This shows that the developed system is very useful for the markerless integration of exogenous genes into the chromosome of gram-negative eubacteria.     

In vivo site-specific integration of transgene in silkworm via PhiC31 integrase-mediated cassette exchange

Current techniques for genetic engineering of the silkworm Bombyx mori genome utilize transposable elements, which result in positional effects and insertional mutagenesis through random insertion of exogenous DNA. New methods for introducing transgenes at specific positions are therefore needed to overcome the limitations of transposon-based strategies. Although site-specific recombination systems have proven powerful tools for genome manipulation in many organisms, their use has not yet been well established for the integration of transgenes in the silkworm. We describe a method for integrating target genes at pre-defined chromosomal sites in the silkworm via phiC31/att site-specific recombination system-mediated cassette exchange. Successful recombinase-mediated cassette exchange (RMCE) was observed in the two transgenic target strains with an estimated transformation efficiency of 3.84–7.01%. Our results suggest that RMCE events between chromosomal attP/attP target sites and incoming attB/attB sites were more frequent than those in the reciprocal direction. This is the first report of in vivo RMCE via phiC31 integrase in the silkworm, and thus represents a key step toward establishing genome manipulation technologies in silkworms and other lepidopteran species.     

纳豆激酶集成化分离技术

综述了纳豆激酶的分离纯化技术的研究现状和发展趋势。通过对常规分离技术的分析,重点讨论了集成化分离技术的应用及其优势,包括集成化双水相分配技术、扩张床吸附技术以及耐盐性混合模式吸附技术等分离方法。并指出集成化分离技术在生产纳豆激酶以及其他活性蛋白方面,具有广阔的应用前景。     

Thoughts on clonal integration: Facing the evolutionary context

Summary In this essay, I have pointed out that the appropriate evolutionary context for plant clonality dictates a focus on the impact of the derived trait of potential independence of subunits on the evolutionarily primitive trait of obligate interdependence of plant subunits, i.e. the advantages of independence. This fact prescribes a major shift in approach from previous lines of investigation which have assumed that clonal plants should fall apart and sought to determine the advantages of interdependence. The delineated reorientation calls for a significant change in the investigation of the ecology of clonality in higher plants, emphasizing factors that select for physical and physiological disintegration of the genet and de-emphasizing the need to derive ecological explanations for properties a plant will possess entirely by reason of its phylogenetic and developmental heritage. I suggest that (1) patterns of ramet independence may result from selective pressures on the cost of interconnections (2) programmed ramet independendence may be a response to the selective pressure of a high possibility of traumatic breakage and (3) programmed ramet independence may allow escape of the genet from mortality due to pathogen infestation.     

The Capture: Kidnapping Students’ Interests Using the Guardians of Ga’Hoole

This project describes a fourth-grade unit that integrated science and language arts using the book The Capture as a focal point. During the unit, students engaged in science activities and language arts lessons that focused on owls. Students conducted investigations that helped them develop a deeper understanding of the adaptations of several owl species. Additionally, the fourth-graders developed their language arts skills for conducting research, using figurative language, and presenting information. Examples of helpful resources and student work are included.     

Data merging for integrated microarray and proteomic analysis.

The functioning of even a simple biological system is much more complicated than the sum of its genes, proteins and metabolites. A premise of systems biology is that molecular profiling will facilitate the discovery and characterization of important disease pathways. However, as multiple levels of effector pathway regulation appear to be the norm rather than the exception, a significant challenge presented by high-throughput genomics and proteomics technologies is the extraction of the biological implications of complex data. Thus, integration of heterogeneous types of data generated from diverse global technology platforms represents the first challenge in developing the necessary foundational databases needed for predictive modelling of cell and tissue responses. Given the apparent difficulty in defining the correspondence between gene expression and protein abundance measured in several systems to date, how do we make sense of these data and design the next experiment? In this review, we highlight current approaches and challenges associated with integration and analysis of heterogeneous data sets, focusing on global analysis obtained from high-throughput technologies.     

Building Developmental Integration into Functional Systems: Function-Induced Integration of Mandibular Shape

The mammalian mandible is a developmentally modular but functionally integrated system. Whether morphological integration can evolve to match the optimal pattern of functional integration may depend on the developmental origin of integration, specifically, on the role that direct epigenetic interactions play in shaping integration. These interactions are hypothesized to integrate modules and also to be highly conservative, potentially constraining the evolution of integration. Using the fox squirrel (Sciurus niger) mandible as a model system, we test five a priori developmental hypotheses that predict mandibular integration and we also explore for correlations between shapes of mandibular regions not anticipated by any of the developmental models. To determine whether direct epigenetic interactions are highly conserved in rodents, we examine the correlation structure of fluctuating asymmetry, and compare integration patterns between fox squirrels and prairie deer mice (Peromyscus maniculatus bairdii). In fox squirrels, we find a correlation structure unanticipated by all a priori developmental models: adjacent parts along the proximodistal jaw axis are correlated whereas more distant ones are not. The most notable exception is that the shape of the anterior incisor alveolus is correlated with the shape of the ramus (FA component) or coronoid (symmetric component). Those exceptions differ between species; in prairie deer mice, the molar alveolus is connected to more parts, and the incisor alveolus to fewer, than in fox squirrels. The structure of integration suggests that the mandible cannot be decomposed into parts but rather is a single connected unit, a result consistent with its functional integration. That match between functional and developmental integration may arise, at least in part, from function-induced growth, building developmental integration into the functional system and enabling direct epigenetic interactions to evolve when function does.     

胚胎发育早期转基因的PCR检测研究

转基因在受精卵中的整合时间对于转基因动物的建立十分重要。采用ＷＡＰ基因调控序列指导的人Ｇ－ＣＳＦ基因为构件,对小鼠受精卵进行显微注射。对培养至１细胞期、２细胞期和８细胞期的胚胎进行ＰＣＲ检测。结果表明,三个时期转基因的检出率分别为１００％、７７．７７％和４４．４４％。说明随着培养时间的增加,转基因逐渐丢失。