A gene regulatory network armature for T lymphocyte specification

Choice of a T lymphoid fate by hematopoietic progenitor cells depends on sustained Notch–Delta signaling combined with tightly regulated activities of multiple transcription factors. To dissect the regulatory network connections that mediate this process, we have used high-resolution analysis of regulatory gene expression trajectories from the beginning to the end of specification, tests of the short-term Notch dependence of these gene expression changes, and analyses of the effects of overexpression of two essential transcription factors, namely PU.1 and GATA-3. Quantitative expression measurements of >50 transcription factor and marker genes have been used to derive the principal components of regulatory change through which T cell precursors progress from primitive multipotency to T lineage commitment. Our analyses reveal separate contributions of Notch signaling, GATA-3 activity, and down-regulation of PU.1. Using BioTapestry (www.BioTapestry.org), the results have been assembled into a draft gene regulatory network for the specification of T cell precursors and the choice of T as opposed to myeloid/dendritic or mast-cell fates. This network also accommodates effects of E proteins and mutual repression circuits of Gfi1 against Egr-2 and of TCF-1 against PU.1 as proposed elsewhere, but requires additional functions that remain unidentified. Distinctive features of this network structure include the intense dose dependence of GATA-3 effects, the gene-specific modulation of PU.1 activity based on Notch activity, the lack of direct opposition between PU.1 and GATA-3, and the need for a distinct, late-acting repressive function or functions to extinguish stem and progenitor-derived regulatory gene expression

The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding sites

The mapper2 Database (http://genome.ufl.edu/mapperdb) is a component of mapper2, a web-based system for the analysis of transcription factor binding sites in multiple genomes. The database contains predicted binding sites identified in the promoters of all human, mouse and Drosophila genes using 1017 probabilistic models representing over 600 different transcription factors. In this article we outline the current contents of the database and we describe its web-based user interface in detail. We then discuss ongoing work to extend the database contents to experimental data and to add analysis capabilities. Finally, we provide information about recent improvements to the hardware and software platform that mapper2 is based on

Effect of Fe-rich intermetallics on tensile behavior of Al-Cu 206 cast alloys at solid and near-solid states

Iron is one of the most common impurity elements in Al-Cu 206 cast alloys as it often causes the precipitation of Fe-rich intermetallic phases during solidification due to its extremely low solid solubility in aluminum. The characteristics of the Fe-rich intermetallics, such as type, morphology, size, and distribution, have significant influences on the tensile behaviors of the Al alloys. In the present work, two Al-Cu 206 cast alloys containing different types of Fe-rich intermetallics (dominated by either platelet β-Fe or Chinese script α-Fe) were cast and their tensile tests were performed at both solid (room temperature) and near-solid (2.8 vol. % liquid) states. It is found that the tensile properties in both solid and near-solid states are improved when the Fe-rich intermetallics change from platelet to Chinese script morphologies. During the solid state tensile deformation, the failure occurs mainly along the platelet β-Fe intermetallics/Al matrix interface or within the Chinese script α-Fe particles. In the near-solid state, the alloy containing mainly Chinese script α-Fe is found to have more free flow paths for liquid feeding, leading to improved tensile properties. By contrast, the platelet β-Fe can cause the blockage of the liquid flow paths, leading to the degraded tensile properties and worsened susceptibility to hot tearing

Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism

Cells respond to fatty acid exposure by metabolic reorganization and proliferation of peroxisomes. Described here is the development and application of a genome-wide screen to identify nonessential yeast genes necessary for efficient metabolism of myristic and oleic acids. Comparison of the resultant fitness data set with an integrated data set of genes transcriptionally responsive to fatty acids revealed very little overlap between the data sets. Furthermore, the fitness data set enriched for genes involved in peroxisome biogenesis and other processes related to cell morphology, whereas the expression data set enriched for genes related to metabolism. These data suggest that in response to fatty acid exposure, transcriptional control is biased towards metabolic reorganization, and structural changes tend to be controlled post-transcriptionally. They also suggest that fatty acid responsive metabolic networks are more robust than those related to cell structure. Statistical analyses of these and other global data sets suggest that the utilization of distinct control mechanisms for the execution of morphological versus metabolic responses is widespread

Low-power density of 950 MHz radiation does not affect long-term potentiation in rat dentate gyrus

Introduction: Over the last decade, exposure to non-ionizing electromagnetic waves due to base station antenna has increased. This in vivo study was planned for evaluating the effects of whole-body exposure to 950 MHz field of GSM mobile phone system on rat dentate gyrus long-term potentiation. Materials and methods: 24 naive male Wistar rats (3 month old, 225±25 g) were randomly divided in the three groups (sham-exposed, GSM and continuous field exposed). The exposure program was planned for 10 sessions at 3 days. Animals were exposed to electromagnetic field for 45 minutes in a circular plastic chamber (mean power density=0.835 mW/cm2). Immediately after end exposure, anesthesia was induced for long term potentiation (LTP) induction. Field potentials were recorded and analyzed using the population spike amplitude and EPSP slope for 60-min. Results; There were no significant differences in population spike amplitude, EPSP slope and EPSP slope maintenance among the three groups. Conclusion: This study provides no evidence indicating that long-term potentiation can be affected by the whole-body exposure to low-power density of 950 MHz field of GSM mobile phone System

Mass spectrometry detection of inhaled drug in distal fibrotic lung

BACKGROUND: Currently the only available therapies for fibrotic Interstitial Lung Disease are administered systemically, often causing significant side effects. Inhaled therapy could avoid these but to date there is no evidence that drug can be effectively delivered to distal, fibrosed lung. We set out to combine mass spectrometry and histopathology with rapid sample acquisition using transbronchial cryobiopsy to determine whether an inhaled drug can be delivered to fibrotic, distal lung parenchyma in participants with Interstitial Lung Disease. METHODS: Patients with radiologically and multidisciplinary team confirmed fibrotic Interstitial Lung Disease were eligible for this study. Transbronchial cryobiopsies and endobronchial biopsies were taken from five participants, with Interstitial Lung Disease, within 70 min of administration of a single dose of nebulised ipratropium bromide. Thin tissue cryosections were analysed by Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry imaging and correlated with histopathology. The remainder of the cryobiopsies were homogenised and analysed by Liquid Chromatography—tandem Mass Spectrometry. RESULTS: Drug was detected in proximal and distal lung samples from all participants. Fibrotic regions were identified in research samples of four of the five participants. Matrix Assisted Laser Desorption/Ionization-Mass Spectrometry imaging showed co-location of ipratropium with fibrotic regions in samples from three participants. CONCLUSIONS: In this proof of concept study, using mass spectrometry, we demonstrate for the first-time that an inhaled drug can deposit in distal fibrotic lung parenchyma in patients with Interstitial Lung Disease. This suggests that drugs to treat pulmonary fibrosis could potentially be administered by the inhaled route

High-performance bio-inspired composite T-joints

This paper introduces a novel bio-inspired design strategy based on the optimised topology of bird bone's joint to improve the strength-to-weight ratio and damage tolerance of composite T-joints. Better structuring the constituents' materials near the sharp bends results in re-distribution of stress over a larger area and reduces the stress concentration. This is done by an integrally formed support structure that is spaced apart from the main body of the T-joint in the vicinity of the bend using a Polyvinyl Chloride (PVC) foam. The support structure acts as a buttress across the bend and improves the performance of the T-joint. The T-joints are fabricated using wet layup process, from 2/2 twill TC35-carbon fibre fabric/SR5550 epoxy resin, and are subjected to quasi-static and fatigue bending, and quasi-static tensile pull-out tests. The quasi-static results reveal that the bio-inspired T-joint design has huge improvements compared to a conventional T-joint in the elastic stiffness (over 60%), peak load (over 40%) and absorbed mechanical energy (over 130%). There is only 3% weight increase in the bio-inspired T-joint compared to the conventional one. The fatigue results show a significant improvement for the bio-inspired design proving the efficiency of the novel bio-inspired design for both quasi-static and cyclic loadings

How to Build Transcriptional Network Models of Mammalian Pattern Formation

Genetic regulatory networks of sequence specific transcription factors underlie pattern formation in multicellular organisms. Deciphering and representing the mammalian networks is a central problem in development, neurobiology, and regenerative medicine. Transcriptional networks specify intermingled embryonic cell populations during pattern formation in the vertebrate neural tube. Each embryonic population gives rise to a distinct type of adult neuron. The homeodomain transcription factor Lbx1 is expressed in five such populations and loss of Lbx1 leads to distinct respecifications in each of the five populations. allele, respectively. Microarrays were used to show that expression levels of 8% of all transcription factor genes were altered in the respecified pool. These transcription factor genes constitute 20–30% of the active nodes of the transcriptional network that governs neural tube patterning. Half of the 141 regulated nodes were located in the top 150 clusters of ultraconserved non-coding regions. Generally, Lbx1 repressed genes that have expression patterns outside of the Lbx1-expressing domain and activated genes that have expression patterns inside the Lbx1-expressing domain.nalysis, and think that it will be generally useful in discovering and assigning network interactions to specific populations. We discuss how ANCEA, coupled with population partitioning analysis, can greatly facilitate the systematic dissection of transcriptional networks that underlie mammalian patterning

Mechanical characterization of high volume fraction Al7075-Al2O3 composite fabricated by semisolid powder processing

The mechanical properties and physical characteristics of aluminum alloy composites can be significantly improved by adding reinforcing phases. However, the high loading of the reinforcement phase in Al7075-Al2O3 composites has not been thoroughly studied. In this work, a combination of semisolid metal powder processing and powder metallurgy is used to process and manufacture Al7075-Al2O3 composites with a high reinforcement fraction of > 40 vol.%. The effects of processing parameters on the microstructures and mechanical properties of the composite material are discussed in detail. The loading limits of the high volume Al2O3 reinforcement in Al7075 composites are identified and linked to the processing parameters. A methodology is introduced to estimate the consolidation temperature of Al7075 alloy using compaction testing. Al2O3 particles (the average particle size of 120 µm) were mechanically milled with Al7075 powder (the average particle size of 20 µm) for 10 min and 5 h using a high-energy planetary ball mill. The mixture was then compacted in the semisolid state at 615 °C under the compaction pressures of 50 MPa and 100 MPa. By increasing the milling time from 10 min to 5 h, the deformation of aluminum powders and the fracture of Al2O3 reinforcement particles occur, restricting the loading limit of reinforcement. The milling time also shows a dominant effect on the powder morphology, microstructure, and mechanical properties of Al7075-Al2O3 composites. Increasing compaction pressure from 50 to 100 MPa significantly improved the compressive strength of the composite from 218 to 652 MPa. Al7075-Al2O3 composite with 40 vol.% of reinforcing phase exhibits the highest hardness of 198.2 HV and 96.9% relative density when it is milled for 5 h and compacted at 100 MPa. However, this composite shows the highest strength of 652 MPa when it is milled for 10 min. By increasing the reinforcing phase to 50 vol.% and 60 vol.%, the hardness, density, and compressive strength of composites decreased. The composites with 60 vol.% of reinforcing phase appeared overloaded. Results show that semisolid metal powder processing has huge potential for the fabrication of high loading Al2O3 in Al7075 matrix with near theoretical density

The Innate Immune Database (IIDB)

<p>Abstract</p> <p>Background</p> <p>As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site <url>http://www.innateImmunity-systemsbiology.org</url>. Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens.</p> <p>Description</p> <p>We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser.</p> <p>Conclusion</p> <p>We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at <url>http://db.systemsbiology.net/IIDB</url>.</p