High Sensitivity TSS Prediction: Estimates of Locations Where TSS Cannot Occur

Although transcription in mammalian genomes can initiate from various genomic positions (e.g., 3′UTR, coding exons, etc.), most locations on genomes are not prone to transcription initiation. It is of practical and theoretical interest to be able to estimate such collections of non-TSS locations (NTLs). The identification of large portions of NTLs can contribute to better focusing the search for TSS locations and thus contribute to promoter and gene finding. It can help in the assessment of 5′ completeness of expressed sequences, contribute to more successful experimental designs, as well as more accurate gene annotation.Using comprehensive collections of Cap Analysis of Gene Expression (CAGE) and other transcript data from mouse and human genomes, we developed a methodology that allows us, by performing computational TSS prediction with very high sensitivity, to annotate, with a high accuracy in a strand specific manner, locations of mammalian genomes that are highly unlikely to harbor transcription start sites (TSSs). The properties of the immediate genomic neighborhood of 98,682 accurately determined mouse and 113,814 human TSSs are used to determine features that distinguish genomic transcription initiation locations from those that are not likely to initiate transcription. In our algorithm we utilize various constraining properties of features identified in the upstream and downstream regions around TSSs, as well as statistical analyses of these surrounding regions.

Wastewater treatment plants as a source of microplastics in river catchments

It is now well established that the oceans contain significant accumulations of plastic debris but only very recently have studies began to look at sources of microplastics (MPs) in river catchments. This work measured MPs up- and downstream of six wastewater treatment plants (WWTPs) in different catchments with varying characteristics and found that all led to an increase in MPs in rivers. Nevertheless, the data collected indicated that there were other important sources of MPs in the catchments studied and that these may include atmospheric deposition, agricultural land to which sewage sludge has been applied, and diffuse release of secondary MPs following the breakdown of larger plastic items. MPs were comprised mainly of fibres, fragments, and flakes with pellets and beads only dominating at one site. Variation in MP pollution occurred over time and this difference was greater at some sites than others. A key research need is the further study of MP sources in river catchments to facilitate management efforts to reduce their presence in freshwater and marine environments

Characterization of an enzymatic packed-bed microreactor: Experiments and modeling

A micro packed-bed reactor (µPBR) based on two-parallel-plates configuration with immobilized Candida antarctica lipase B in the form of porous particles (Novozym® 435) was theoretically and experimentally characterized. A residence time distribution (RTD) within µPBRs comprising various random distributions of particles placed in one layer was computationally predicted by a mesoscopic lattice Boltzmann (LB) method. Numerical simulations were compared with measurements of RTD, obtained by stimulus-response experiment with a pulse input using glucose as a tracer, monitored by an electrochemical glucose oxidase microbiosensor integrated with the reactor. The model was validated by a good agreement between the experimental data and predictions of LB model at different conditions. The developed µPBR was scaled-up in length and width comprising either a single or two layers of Novozym® 435 particles and compared regarding the selected enzyme-catalyzed transesterification. A linear increase in the productivity with the increase in all dimensions of the µPBR between two-plates demonstrated very efficient and simple approach for the capacity rise. Further characterization of µPBRs of various sizes using the piezoresistive pressure sensor revealed very low pressure drops as compared to their conventional counterparts and thereby great applicability for production systems based on numbering-up approach

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

Motivation: More and more genomes are being sequenced, and to keep up with the pace of sequencing projects, automated annotation techniques are required. One of the most challenging problems in genome annotation is the identification of the core promoter. Because the identification of the transcription initiation region is such a challenging problem, it is not yet a common practice to integrate transcription start site prediction in genome annotation projects. Nevertheless, better core promoter prediction can improve genome annotation and can be used to guide experimental work

RBF-TSS: Identification of Transcription Start Site in Human Using Radial Basis Functions Network and Oligonucleotide Positional Frequencies

Accurate identification of promoter regions and transcription start sites (TSS) in genomic DNA allows for a more complete understanding of the structure of genes and gene regulation within a given genome. Many recently published methods have achieved high identification accuracy of TSS. However, models providing more accurate modeling of promoters and TSS are needed. A novel identification method for identifying transcription start sites that improves the accuracy of TSS recognition for recently published methods is proposed. This method incorporates a metric feature based on oligonucleotide positional frequencies, taking into account the nature of promoters. A radial basis function neural network for identifying transcription start sites (RBF-TSS) is proposed and employed as a classification algorithm. Using non-overlapping chunks (windows) of size 50 and 500 on the human genome, the proposed method achieves an area under the Receiver Operator Characteristic curve (auROC) of 94.75% and 95.08% respectively, providing increased performance over existing TSS prediction methods

Short-term facilitation and depression in the cerebellum: some observations on wild-type and mutant rodents deficient in the extracellular matrix molecule tenascin C

Short-term plasticity was studied on synapses to Purkinje cells (PC): paired-pulse facilitation in parallel fibers (PF) and paired-pulse depression in climbing fibers (CF). Both phenomena relate to synaptic strength. These forms of short-term plasticity were tested on cerebellar slices in rat by early postnatal synchronous stimulation of olivary neurons (i.e., CFs) with harmaline and by inhibition of a metabotropic glutamate receptor (mGluR) as well as in mice that were deficient in the extracellular matrix glycoprotein tenascin-C. Harmaline stimulation delayed the developmental competition between CF inputs and maintained multiple innervation. Paired-pulse depression of the CF-PC synapse after harmaline treatment was more expressed. However, paired-pulse facilitation in PF-PC synapses remained unchanged. Electrophysiological responses of postsynaptic mGluR1 in CF-PC synapses could be obtained only with AMPA receptors blocked and glutamate uptake impaired. The mGluR1-specific antagonist CPCCOEt suppressed the CF-mGluR EPSC in some PCs and potentiated it in other PCs. CF paired-pulse depression was not changed with CPCCOEt, thus excluding a presynaptic effect. The postsynaptic effect was underlined by CPCCOEt-induced rise in amplitude of EPSC and by a prolongation of its decay time. Tenascins are extracellular matrix glycoproteins that may restrict the regenerative capacity of the nervous tissue. Testing short-term presynaptic plasticity in tenascin-C-deficient mice showed that CF paired-pulse depression was less expressed while PF paired-pulse facilitation was augmented except in a group of cells where there was even depression. The results underline differences in forms of short-term plasticity with regard to susceptibility to diverse modulatory factors

Testing of a Continuous Sampling Mercury CEM at the EPA-Rotary Kiln Incinerator Simulator Facility

This report has been prepared to document the performance of the continuous sampling mercury monitoring system developed by Ames Laboratory for use as a continuous emission monitor (CEM). This work was funded by the U.S. Department of Energy, Office of Environmental Management, Office of Science and Technology, through the Mixed Waste Focus Area. The purpose of the project is to develop instrumentation and methods for spectroscopic field-monitoring applications. During FY01 this included continued development and testing of an echelle spectrometer system for the detection of mercury (Hg) by atomic absorption. Due to the relatively poor limits of detection for Hg by optical emission techniques, the CEM has been designed for the detection of elemental Hg by optical absorption. The sampling system allows continuous introduction of stack gas into the CEM for analysis of elemental and total Hg in the gas stream. A heated pyrolysis tube is used in this system to convert oxidized Hg compounds to elemental Hg prior to analysis for total Hg. The pyrolysis tube is bypassed to measure elemental Hg. The CEM is designed to measure the elemental Hg concentration of the gas sample, measure the total Hg concentration, perform a zero check (analysis of room air), and then re-zero the system (to correct for any instrumental drift that occurs over time). This is done in an automated, sequential measurement cycle to provide continuous monitoring of Hg concentrations in the stack gas. The continuous sampling Hg CEM was tested at the EPA-Rotary Kiln in Durham, NC at the beginning of FY02. This report describes the characteristics and performance of the system and the results of the field tests performed at EPA. The Hg CEM system was developed in response to the need of DOE and other organizations to monitor Hg that may be released during the processing or combustion of hazardous or mixed-waste materials. The promulgation of regulations limiting the release of Hg and requiring continuous monitoring of stack gases from combustion and treatment processes would seriously impact the operations of DOE waste treatment facilities. Therefore, it is important to develop and validate techniques that adequately meet proposed sensitivity and accuracy requirements. The most likely form of validation for such a technique involves comparison of CEM results with a reference test method for a test combustion system. Therefore, the CEM system was tested at EPA by monitoring Hg emissions in a natural gas combustion exhaust (that was spiked with Hg) while simultaneously collecting samples using the Ontario-Hydro mercury speciation method as the reference method. The CEM results were available continuously during the on-line monitoring that was performed. The results of the reference method sampling were received a number of weeks after the testing at EPA. These results are discussed in this report, with a comparison and evaluation of the reference method and Hg CEM data