A comparative analysis of transcription factor expression during metazoan embryonic development

During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which are following the expression and activity of transcription factors (TFs). This study sought to compare TF expression during embryonic development in a diverse group of metazoan animals: representatives of vertebrates (Danio rerio, Xenopus tropicalis), a chordate (Ciona intestinalis) and invertebrate phyla such as insects (Drosophila melanogaster, Anopheles gambiae) and nematodes (Caenorhabditis elegans) were sampled, The different species showed overall very similar TF expression patterns, with TF expression increasing during the initial stages of development. C2H2 zinc finger TFs were over-represented and Homeobox TFs were under-represented in the early stages in all species. We further clustered TFs for each species based on their quantitative temporal expression profiles. This showed very similar TF expression trends in development in vertebrate and insect species. However, analysis of the expression of orthologous pairs between more closely related species showed that expression of most individual TFs is not conserved, following the general model of duplication and diversification. The degree of similarity between TF expression between Xenopus tropicalis and Danio rerio followed the hourglass model, with the greatest similarity occuring during the early tailbud stage in Xenopus tropicalis and the late segmentation stage in Danio rerio. However, for Drosophila melanogaster and Anopheles gambiae there were two periods of high TF transcriptome similarity, one during the Arthropod phylotypic stage at 8-10 hours into Drosophila development and the other later at 16-18 hours into Drosophila development.Comment: ~10 pages, 50 references, 6+3 figures and 5 table

A strategy for achieving manufacturing statistical process control within a highly complex aerospace environment

This paper presents a strategy to achieve process control and overcome the previously mentioned industry constraints by changing the company focus to the process as opposed to the product. The strategy strives to achieve process control by identifying and controlling the process parameters that influence process capability followed by the implementation of a process control framework that marries statistical methods with lean business process and change management principles. The reliability of the proposed strategy is appraised using case study methodology in a state of the art manufacturing facility on Multi-axis CNC machine tools

BioSAVE: display of scored annotation within a sequence context.

BACKGROUND: Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. RESULTS: We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation) within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains) from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. CONCLUSION: Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The developmental expression dynamics of Drosophila melanogaster transcription factors.

BACKGROUND: Site-specific transcription factors (TFs) are coordinators of developmental and physiological gene expression programs. Their binding to cis-regulatory modules of target genes mediates the precise cell- and context-specific activation and repression of genes. The expression of TFs should therefore reflect the core expression program of each cell. RESULTS: We studied the expression dynamics of about 750 TFs using the available genomics resources in Drosophila melanogaster. We find that 95% of these TFs are expressed at some point during embryonic development, with a peak roughly between 10 and 12 hours after egg laying, the core stages of organogenesis. We address the differential utilization of DNA-binding domains in different developmental programs systematically in a spatio-temporal context, and show that the zinc finger class of TFs is predominantly early expressed, while Homeobox TFs exhibit later expression in embryogenesis. CONCLUSIONS: Previous work, dissecting cis-regulatory modules during Drosophila development, suggests that TFs are deployed in groups acting in a cooperative manner. In contrast, we find that there is rapid exchange of co-expressed partners amongst the fly TFs, at rates similar to the genome-wide dynamics of co-expression clusters. This suggests there may also be a high level of combinatorial complexity of TFs at cis-regulatory modules.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

El habitar, la animalidad y lo visible de los objetos. Cultura material y pragmática de lo visible en un hogar de Bogotá

Este artículo explora las relaciones entre la apropiación de objetos de uso en uno de los espacios del hogar y la construcción y reproducción de significaciones culturales en la vida cotidiana. Se plantea que dicha relación se encuentra atravesada por maneras de hacer visibles dichas significaciones mediante la materialidad de los objetos, con el fin de sostener un proceso creativo por parte del individuo sobre su propia existencia. Para ello, se realiza el análisis de un caso de sala de un hogar en la ciudad de Bogotá haciendo énfasis en una pragmática de lo visible a través del concepto de “acto de visión” con base en las relaciones entre los objetos del caso analizado.This paper explores the relationships between the appropriation of objects of use in one of the areas of the home and the construction and reproduction of cultural meanings in everyday life. It is argued that this relationship is crossed by ways to make visible these meanings trough the materiality of objects, in order to sustain a creative process by the individual over his own existence. For this, it presents the analysis of a case of living room in the city of Bogotá emphasizing in a pragmatic of the visible through the concept of “act of vision” based on the relationships between the objects found in the analyzed case

Pengaruh Faktor Bermukim Masyarakat Terhadap Pola Persebaran Permukiman di Kawasan Rawan Bencana Longsor Kabupaten Magetan

Perumahan dan permukiman merupakan kebutuhan mendasar manusia untuk melakukan aktivitas sehari-hari demi kelangsungan hidup manusia. Perumahan dan permukiman mempunyai fungsi dan peranan yang penting dalam kehidupan manusia, perumahan merupakan pencerminan dari jati diri pribadi manusia. Permukiman merupakan tempat hidup manusia dan melakukan berbagai macam aktivitas yang di dalamnya tersedia sarana dan prasarana penunjang dan lapangan pekerjaan untuk kegiatan sehari-hari masyarakat yang tinggal di kawasan permukiman tersebut hal tersebut dapat mempengaruhi masyarakat dalam membentuk kawasan permukiman dengan bentuk yang berbeda-beda. Pola permukiman dapat diartikan sebagai suatu tempat atau suatu daerah tempat penduduk berkumpul dan hidup bersama, menggunakan lingkungan setempat untuk mempertahankan, melangsungkan dan mengembangkan hidupnya, pola permukiman memiliki variasi pola dari yang sangat jarang hingga sangat padat, mengelompok, teratur dan tidak teratur. Masyarakat dalam menentukan lokasi permukiman memiliki dasar pertimbangan yang mempengaruhi mereka dalam memilih lokasi untuk bermukim. Dasar pertimbangan tersebut terdiri dari beberapa faktor, antara lain aksesibilitas, lingkungan, peluang kerja, tingkat pelayanan, selain itu faktor psikologis, faktor sosial ekonomi dan faktor kultural historis. Kawasan lereng Gunung Lawu yang memiliki topografi dan kontur yang rapat membuat pola permukiman yang berada di kawasan tersebut sebagian besar secara mengelompok serta jarak antara kelompok satu dengan lain yang berjauhan. Terdapat beberapa faktor yang mempengaruhi terbentuknya pola permukiman yaitu ekonomi, budaya, kelembagaan dan adat istiadat. Bencana longsor merupakan bencana yang mengancam kelangsungan hidup manusia yang bermukim di daerah tersebut. Bahaya bencana merupakan suatu fenomena alam atau buatan yang mempunyai potensi mengancam kehidupan manusia, kerugian harta benda dan kerusakan lingkungan. Pada dasarnya letak permukiman maupun perumahan tidak diperbolehkan berada pada daerah lereng gunung yang berpotensi terjadi bencana longsor. Masyarakat memiliki pertimbangan-pertimbangan sendiri terhadap pemilihan lokasi bermukim yang menjadikan lereng gunung menjadi pilihan bermukim dan menjadi terhadap terbentuknya pola permukiman di Kecamatan Poncol dan Plaosan Kabupaten Magetan yang berada di lereng Gunung Lawu. Kata Kunci: permukiman, faktor bermukim, pola persebaran permukiman, pegunungan, tanah longso

The Influence of Transcription Factor Competition on the Relationship between Occupancy and Affinity

Transcription factors (TFs) are proteins that bind to specific sites on the DNA and regulate gene activity. Identifying where TF molecules bind and how much time they spend on their target sites is key to understanding transcriptional regulation. It is usually assumed that the free energy of binding of a TF to the DNA (the affinity of the site) is highly correlated to the amount of time the TF remains bound (the occupancy of the site). However, knowing the binding energy is not sufficient to infer actual binding site occupancy. This mismatch between the occupancy predicted by the affinity and the observed occupancy may be caused by various factors, such as TF abundance, competition between TFs or the arrangement of the sites on the DNA. We investigated the relationship between the affinity of a TF for a set of binding sites and their occupancy. In particular, we considered the case of the transcription factor lac repressor (lacI) in E.coli, and performed stochastic simulations of the TF dynamics on the DNA for various combinations of lacI abundance and competing TFs that contribute to macromolecular crowding. We also investigated the relationship of site occupancy and the information content of position weight matrices (PWMs) used to represent binding sites. Our results showed that for medium and high affinity sites, TF competition does not play a significant role for genomic occupancy except in cases when the abundance of the TF is significantly increased, or when the PWM displays relatively low information content. Nevertheless, for medium and low affinity sites, an increase in TF abundance (for both cognate and non-cognate molecules) leads to an increase in occupancy at several sites. © 2013 Zabet et al

ANALISIS PENGARUH KUALITAS SITUS WEB TERHADAP NIAT BERPERILAKU KONSUMEN, DENGAN KEPUASAN ELEKTRONIK SEBAGAI VARIABEL INTERVENING PADA E-COMMERCE DI SEMARANG (Studi pada pengguna Online Shop Jakartanotebook)

This study aimed to analyze the effect arising from the usefulness, ease of use, enjoyment and e-trust on satisfaction and its influence on behavioural intention from website Jakartanotebook.com. The variables used in this study is usefulness, ease of use, enjoyment, and e-trust as an independent variable, then e-satisfaction as an intervening variable lastly, behavioural intention as the dependent variable. The sample in this study were 125 respondents that came from the consumer of online shop Jakartanotebook in Semarang. The method used is non-porbability sampling by distribusting questionnaires to the respondents(consumer of online shop Jakartanotebook in Semarang). In this study developed a theoretical model to propose six hypotheses to be tested using analysis tools Structural Equation Modeling (SEM) which is operated through a program AMOS 22.0. Based on the research of data processing SEM for full model has met the criteria of goodness of fit as follows, the value of chi-square = 253,771; probability = 0,053; RMSEA = 0,036; CMIN/DF = 1,159; GFI = 0,855; TLI = 0,970; CFI = 0,974, and a marginal criteria which is AGFI = 0,817. With the result, it can be said that this model is feasible to be used. The results showed that the behavioural intention can be improved by increasing usefulness, ease of use, enjoymeny, and e-trust that affect the e-satisfaction as a determinant of success to increase behavioural intention

Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data.

Many genes are expressed in bursts, which can contribute to cell-to-cell heterogeneity. It is now possible to measure this heterogeneity with high throughput single cell gene expression assays (single cell qPCR and RNA-seq). These experimental approaches generate gene expression distributions which can be used to estimate the kinetic parameters of gene expression bursting, namely the rate that genes turn on, the rate that genes turn off, and the rate of transcription. We construct a complete pipeline for the analysis of single cell qPCR data that uses the mathematics behind bursty expression to develop more accurate and robust algorithms for analyzing the origin of heterogeneity in experimental samples, specifically an algorithm for clustering cells by their bursting behavior (Simulated Annealing for Bursty Expression Clustering, SABEC) and a statistical tool for comparing the kinetic parameters of bursty expression across populations of cells (Estimation of Parameter changes in Kinetics, EPiK). We applied these methods to hematopoiesis, including a new single cell dataset in which transcription factors (TFs) involved in the earliest branchpoint of blood differentiation were individually up- and down-regulated. We could identify two unique sub-populations within a seemingly homogenous group of hematopoietic stem cells. In addition, we could predict regulatory mechanisms controlling the expression levels of eighteen key hematopoietic transcription factors throughout differentiation. Detailed information about gene regulatory mechanisms can therefore be obtained simply from high throughput single cell gene expression data, which should be widely applicable given the rapid expansion of single cell genomics.This work was supported by: Royal Society Research Fellowship, Marshall Scholarship, Medical Research Council, the Leukemia and Lymphoma Society and core support grants from the Wellcome Trust to the Cambridge Institute for Medical Research and the Wellcome Trust and MRC Cambridge Stem Cell Institute.This is the final version of the article. It first appeared from the Public Library of Science via http://dx.doi.org/10.1371/journal.pcbi.100507