Cell type-specific profiling of protein-DNA interactions without cell isolation using Targeted DamID with next-generation sequencing

The ability to profile transcription and chromatin binding in a cell type-specific manner is a powerful approach for understanding cell fate specification and cellular function in multicellular organisms. We recently developed Targeted DamID (TaDa) to enable genome-wide, cell-type-specific profiling of DNA- and chromatin-binding proteins in vivo without cell isolation. As a Protocol Extension, this article describes substantial modifications to an existing Protocol and offers additional applications. TaDa builds upon DamID, a technique for detecting genome-wide DNA binding profiles of proteins, by coupling it with the GAL4 system in Drosophila to enable both temporal and spatial resolution. TaDa ensures that Dam-fusion proteins are expressed at very low levels, avoiding toxicity and potential artefacts from over-expression. The modifications to the core DamID technique presented here also increase the speed of sample processing and throughput, and adapt the method to Nextgeneration Sequencing technology. TaDa is robust, reproducible, and highly sensitive. Compared to other methods for cell-type specific profiling, the technique requires no cell-sorting, crosslinking or antisera, and binding profiles can be generated from as few as 10,000 total induced cells. By profiling the genome-wide binding of RNA polymerase II, TaDa can also identify transcribed genes in a cell type-specific manner. Here we describe a detailed protocol for carrying out TaDa experiments and preparing the material for next generation sequencing. Although we developed TaDa in Drosophila, it should be easily adapted to other organisms with an inducible expression system. Once transgenic animals are obtained, the entire experimental procedure – from collecting tissue samples to generating sequencing libraries – can be accomplished within 5 days

Collaboration with general practitioners: preferences of medical specialists – a qualitative study

BACKGROUND: Collaboration between general practitioners (GPs) and specialists has been the focus of many collaborative care projects during the past decade. Unfortunately, quite a number of these projects failed. This raises the question of what motivates medical specialists to initiate and continue participating with GPs in new collaborative care models. The following question is addressed in this study: What motivates medical specialists to initiate and sustain new models for collaborating with GPs? METHODS: We conducted semi-structured interviews with eighteen medical specialists in the province of Groningen, in the North of The Netherlands. The sampling criteria were age, gender, type of hospital in which they were practicing, and specialty. The interviews were recorded, fully transcribed, and analysed by three researchers working independently. The resulting motivational factors were grouped into categories. RESULTS: 'Teaching GPs' and 'regulating patient flow' (referrals) appeared to dominate when the motivational factors were considered. In addition, specialists want to develop relationships with the GPs on a more personal level. Most specialists believe that there is not much they can learn from GPs. 'Lack of time', 'no financial compensation', and 'no support from colleagues' were considered to be the main concerns to establishing collaborative care practices. Additionally, projects were often experienced as too complex and time consuming whereas guidelines were experienced as too restrictive. CONCLUSION: Specialists are particularly interested in collaborating because the GP is the gatekeeper for access to secondary health care resources. Specialists feel that they are able to teach the GPs something, but they do not feel that they have anything to learn from the GPs. With respect to professional expertise, therefore, specialists do not consider GPs as equals. Once personal relationships with the GPs have been established, an informal network with incidental professional contact seems to be sufficient to satisfy the collaborative needs of the specialist. The concerns seem to outweigh any positive motivational forces to developing new models of collaborative practice

A post-labeling method for multiplexed and multicolored genotyping analysis of SSR, indel and SNP markers in single tube with bar-coded split tag (BStag)

<p>Abstract</p> <p>Background</p> <p>Genotyping analysis using capillary DNA sequencing with fluorescently labeled primer pairs obtained by polymerase chain reaction (PCR) is widely used, but is expensive. The post-PCR labeling method using fluorescently labeled short oligonucleotides and nested PCR of the amplified product obtained from unlabeled primer pairs is a simple and inexpensive alternative. However, previously reported protocols often produced spurious peaks or inconsistent amplification under multiplexed analysis as a result of simultaneous progress of both the amplification and labeling reactions and local homology of the attached tag sequence.</p> <p>Results</p> <p>A set of 16 bp-long oligonucleotide sequences termed bar-coded split tag (BStag), comprising a common basal region, a three-nucleotide 'bar-code' sequence, and a mismatched nucleotide at the middle position were designed for selective post-PCR labeling. The BStag was attached at the 5' end of the forward primer of interest. The melting temperature of the BStag was low enough to separate the labeling reaction from initial PCR amplification, and each sequence was minimally divergent but maintained maximum selectivity. Post-PCR labeling of the amplified product was achieved by extending for three cycles at a lower annealing temperature after the conventional amplification program with the appropriate fluorescently labeled BStag primer. No amplification was confirmed with BStag primers for 12 plant species. The electropherogram of the labeled product obtained using this method was consistent with that of prelabeled primer, except for their apparent size.</p> <p>Conclusions</p> <p>BStag enabled multiplexed post-PCR labeling of simple sequence repeat or insertion/deletion markers with different dyes in a single tube. BStag in conjunction with locus specific oligo and allele specific oligo was also useful for single nucleotide polymorphism analysis. The labeling protocol was simple and no additional operation was required. Single-tube multiplexed post-PCR labeling is useful for a wide variety of genotyping studies with maximal flexibility and minimal costs.</p

DNA content of a functioning chicken kinetochore

© The Author(s) 2014. In order to understand the three-dimensional structure of the functional kinetochore in vertebrates, we require a complete list and stoichiometry for the protein components of the kinetochore, which can be provided by genetic and proteomic experiments. We also need to know how the chromatin-containing CENP-A, which makes up the structural foundation for the kinetochore, is folded, and how much of that DNA is involved in assembling the kinetochore. In this MS, we demonstrate that functioning metaphase kinetochores in chicken DT40 cells contain roughly 50 kb of DNA, an amount that corresponds extremely closely to the length of chromosomal DNA associated with CENP-A in ChIP-seq experiments. Thus, during kinetochore assembly, CENP-A chromatin is compacted into the inner kinetochore plate without including significant amounts of flanking pericentromeric heterochromatin. © 2014 The Author(s).Wellcome Trust [grant number 073915]; Wellcome Trust Centre for Cell Biology (core grant numbers 077707 and 092076); Darwin Trust of Edinburg

Ecological implications of a flower size/number trade-off in tropical forest trees

Peer reviewedPublisher PD

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

The centromere is a functional chromosome domain that is essential for faithful chromosome segregation during cell division and that can be reliably identified by the presence of the centromere-specific histone H3 variant CenH3. In monocentric chromosomes, the centromere is characterized by a single CenH3-containing region within a morphologically distinct primary constriction. This region usually spans up to a few Mbp composed mainly of centromere-specific satellite DNA common to all chromosomes of a given species. In holocentric chromosomes, there is no primary constriction; the centromere is composed of many CenH3 loci distributed along the entire length of a chromosome. Using correlative fluorescence light microscopy and high-resolution electron microscopy, we show that pea (Pisum sativum) chromosomes exhibit remarkably long primary constrictions that contain 3-5 explicit CenH3-containing regions, a novelty in centromere organization. In addition, we estimate that the size of the chromosome segment delimited by two outermost domains varies between 69 Mbp and 107 Mbp, several factors larger than any known centromere length. These domains are almost entirely composed of repetitive DNA sequences belonging to 13 distinct families of satellite DNA and one family of centromeric retrotransposons, all of which are unevenly distributed among pea chromosomes. We present the centromeres of Pisum as novel ``meta-polycentric'' functional domains. Our results demonstrate that the organization and DNA composition of functional centromere domains can be far more complex than previously thought, do not require single repetitive elements, and do not require single centromere domains in order to segregate properly. Based on these findings, we propose Pisum as a useful model for investigation of centromere architecture and the still poorly understood role of repetitive DNA in centromere evolution, determination, and function

Motives and preferences of general practitioners for new collaboration models with medical specialists: a qualitative study

BACKGROUND: Collaboration between general practitioners (GPs) and specialists has been the focus of many collaborative care projects during the past decade. Unfortunately, quite a number of these projects failed. This raises the question of what motivates GPs to initiate and continue participating with medical specialists in new collaborative care models. The following two questions are addressed in this study: What motivates GPs to initiate and sustain new models for collaborating with medical specialists? What kind of new collaboration models do GPs suggest? METHODS: A qualitative study design was used. Starting in 2003 and finishing in 2005, we conducted semi-structured interviews with a purposive sample of 21 Dutch GPs. The sampling criteria were age, gender, type of practice, and practice site. The interviews were recorded, fully transcribed, and analysed by two researchers working independently. The resulting motivational factors and preferences were grouped into categories. RESULTS: 'Developing personal relationships' and 'gaining mutual respect' appeared to dominate when the motivational factors were considered. Besides developing personal relationships with specialists, the GPs were also interested in familiarizing specialists with the competencies attached to the profession of family medicine. Additionally, they were eager to increase their medical knowledge to the benefit of their patients. The GPs stated a variety of preferences with respect to the design of new models of collaboration. CONCLUSION: Developing personal relationships with specialists appeared to be one of the dominant motives for increased collaboration. Once the relationships have been formed, an informal network with occasional professional contact seemed sufficient. Although GPs are interested in increasing their knowledge, once they have reached a certain level of expertise, they shift their focus to another specialty. The preferences for new collaboration models are diverse. A possible explanation for the differences in the preferences is that professionals are more knowledge driven than organisation driven as the acquiring of new knowledge is considered more important than the route by which this is achieved. A new collaboration model seems a way to acquire knowledge. Once this is achieved the importance of a model possibly diminishes, whereas the professional relationships last