A Primer on Regression Methods for Decoding cis-Regulatory Logic

The rapidly emerging field of systems biology is helping us to understand the molecular determinants of phenotype on a genomic scale [1]. Cis-regulatory elements are major sequence-based determinants of biological processes in cells and tissues [2]. For instance, during transcriptional regulation, transcription factors (TFs) bind to very specific regions on the promoter DNA [2,3] and recruit the basal transcriptional machinery, which ultimately initiates mRNA transcription (Figure 1A). Learning cis-Regulatory Elements from Omics Data A vast amount of work over the past decade has shown that omics data can be used to learn cis-regulatory logic on a genome-wide scale [4-6]--in particular, by integrating sequence data with mRNA expression profiles. The most popular approach has been to identify over-represented motifs in promoters of genes that are coexpressed [4,7,8]. Though widely used, such an approach can be limiting for a variety of reasons. First, the combinatorial nature of gene regulation is difficult to explicitly model in this framework. Moreover, in many applications of this approach, expression data from multiple conditions are necessary to obtain reliable predictions. This can potentially limit the use of this method to only large data sets [9]. Although these methods can be adapted to analyze mRNA expression data from a pair of biological conditions, such comparisons are often confounded by the fact that primary and secondary response genes are clustered together--whereas only the primary response genes are expected to contain the functional motifs [10]. A set of approaches based on regression has been developed to overcome the above limitations [11-32]. These approaches have their foundations in certain biophysical aspects of gene regulation [26,33-35]. That is, the models are motivated by the expected transcriptional response of genes due to the binding of TFs to their promoters. While such methods have gathered popularity in the computational domain, they remain largely obscure to the broader biology community. The purpose of this tutorial is to bridge this gap. We will focus on transcriptional regulation to introduce the concepts. However, these techniques may be applied to other regulatory processes. We will consider only eukaryotes in this tutorial

Protic Ionic Liquids Used as Metal-Forming Green Lubricants for Aluminum: Effect of Anion Chain Length

Among the applications for protic ionic liquids (PILs), lubrication is one of the newest and the most promising. In this work, ammonium-based protic ionic liquids were tested as lubricant fluids for aluminum-steel contacts. PILs were synthesized with 2-hydroxyethylamine (2HEA) and a carboxylic acid (formic and pentanoic), aiming to understand the effect of two different anion chain lengths on the lubricant behavior. The synthesized PILs were characterized by RMN, FTIR and TGA. Wear tests, conducted using a ball-on-plate configuration, showed that the increase of the anion carbon chain length in the PIL structure reduced significantly the coefficient of friction value. Besides, after the wear tests, the PILs structural integrity was not affected. In the same way, bending under tension (BUT) tests evidenced that the performance for stamping conditions of the PIL with the longest anion carbon chain was similar to that of the commercial lubricant. Since, both formed a uniform tribofilm, developed the same lubrication regime and the drawing forces values were close and constant. Hence, the ionic liquid obtained with 2HEA and pentanoic acid (2HEAPe) is as suitable as the commercial lubricant for metal forming processes

Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases

The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular "reactive oxygen species" (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation). The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible. This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference

Monitoring foreign protein expression under baculovirus p10 and polh promoters in insect larvae

X118sciescopu

Insect larval expression process is optimized by generating fusions with green fluorescent protein

The insect larvae/baculovirus protein production process was dramatically simplified by expressing fusion proteins containing green fluorescent protein (GFP) and the product-of-interest. In this case, human interleukin-2 (hlL-2) and chloramphenicol acetyltransferase (CAT) were model products. Specificially, our fusion construct was comprised of a histidine affinity ligand for simplified purification using immobilized metal affinity chromatography (IMAC), the UV-optimized GFP (GFPuv) as a marker, an enterokinase cleavage site for recovery of the product from the fusion, and the product, hIL-2 or CAT. Both the similar to 52 kDa GFPuv/hIL-2 and similar to 63 kDa GFPuV/CAT fusions were expressed in Trichoplusia ni larvae at 9.0 mu g-hIL-2 and 24.1 mu g-CAT per larva, respectively. The GFP enabled clear identification of the infection process, harvest time, and more importantly, the quantity of product protein. Because the GFP served as a marker, this technique obviates the need for in-process Western analyses (during expression, separation, and purification stages). As a purification marker, GFP facilitated rapid identification of product-containing elution fractions (Cha et al., 1999b), as well as product-containing waste fractions (e.g., cell pellet). Also, because the fluorescence intensity was linear with hIL-2 and CAT, we were able to select the highest-producing larvae. That is, three fold more product was found in the brightest larva compared to the average. Finally, because the GFP is attached to the product protein and the producing larvae can be selected, the infection and production processes can be made semi-continuous or continuous, replacing the current batch process. These advantages should help to enable commercialization of larvae as expression hosts. (C) 1999 John Wiley & Sons, Inc.X1140sciescopu

Comparative production of human interleukin-2 fused with green fluorescent protein in several recombinant expression systems

The selection of an optimal recombinant expression system is important for successful protein production. Here, we compared production of human interleukin-2 (hIL-2)-green fluorescent protein (GFP) fusion proteins in several expression systems such as bacteria Escherichia coli, yeast Pichia pastoris, insect Spodoptera frugiperda Sf-9 cells, insect Tricoplusia ni larvae, and insect Drosophila melanogaster S2 cells. Due to the highly hydrophobic nature of hIL-2, the GFP/hIL-2 fusion protein was expressed as an inclusion body in the E coli system, resulting in minimal green fluorescence; however, Western blot analysis revealed the proper fusion band. In all other cases, the fusion proteins were expressed intracellularly or secreted as a functional form; green fluorescence was observed in each of these expression systems. We determined the linear relationships between GFP fluorescence and hIL-2 concentration in each case and used these correlations for comparison of the various expression systems in terms of production yield, productivity, product solubility (for intracellular expression systems), secretion efficiency (for secretion systems), and even functionality by simple measurement of GFP fluorescence. Even though the culture conditions were not optimized for each expression system, this comparison can be used as preliminary criteria for the selection of a proper expression system for recombinant protein production. (C) 2005 Elsevier B.V. All rights reserved.X118sciescopu