The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions.

The Escherichia coli RutR protein is the master regulator of genes involved in pyrimidine catabolism. Here we have used chromatin immunoprecipitation in combination with DNA microarrays to measure the binding of RutR across the chromosome of exponentially growing E. coli cells. Twenty RutR-binding targets were identified and analysis of these targets generated a DNA consensus logo for RutR binding. Complementary in vitro binding assays showed high-affinity RutR binding to 16 of the 20 targets, with the four low-affinity RutR targets lacking predicted key binding determinants. Surprisingly, most of the DNA targets for RutR are located within coding segments of the genome and appear to have little or no effect on transcript levels in the conditions tested. This contrasts sharply with other E. coli transcription factors whose binding sites are primarily located in intergenic regions. We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness

Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data

The transcription of a gene from its DNA template into an mRNA molecule is the first, and most heavily regulated, step in gene expression. Especially in bacteria, regulation is typically achieved via the binding of a transcription factor (protein) or small RNA molecule to the chromosomal region upstream of a regulated gene. The protein or RNA molecule recognizes a short, approximately conserved sequence within a gene's promoter region and, by binding to it, either enhances or represses expression of the nearby gene. Since the sought-for motif (pattern) is short and accommodating to variation, computational approaches that scan for binding sites have trouble distinguishing functional sites from look-alikes. Many computational approaches are unable to find the majority of experimentally verified binding sites without also finding many false positives. Phyloscan overcomes this difficulty by exploiting two key features of functional binding sites: (i) these sites are typically more conserved evolutionarily than are non-functional DNA sequences; and (ii) these sites often occur two or more times in the promoter region of a regulated gene. The website is free and open to all users, and there is no login requirement. Address: (http://bayesweb.wadsworth.org/phyloscan/)

Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present release, aiming for more when information becomes available, (ii) the coverage of the three compartments involved in the silencing process (i.e. targets, miRNA precursors and silencing machinery), (iii) contextual information that enables users to prioritize candidate ‘Patrocles DSPs’, including graphical information on miRNA-target coexpression and eQTL effect of genotype on target expression levels, (iv) the inclusion of Copy Number Variants and eQTL information that affect miRNA precursors as well as genes encoding components of the silencing machinery and (v) a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on ‘Patrocles single nucleotide polymorphisms (pSNPs)’ in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep

Novel variants in the PRDX6 Gene and the risk of Acute Lung Injury following major trauma

<p>Abstract</p> <p>Background</p> <p>Peroxiredoxin 6 (<it>PRDX6</it>) is involved in redox regulation of the cell and is thought to be protective against oxidant injury. Little is known about genetic variation within the PRDX6 gene and its association with acute lung injury (ALI). In this study we sequenced the <it>PRDX6 </it>gene to uncover common variants, and tested association with ALI following major trauma.</p> <p>Methods</p> <p>To examine the extent of variation in the <it>PRDX6 </it>gene, we performed direct sequencing of the 5' UTR, exons, introns and the 3' UTR in 25 African American cases and controls and 23 European American cases and controls (selected from a cohort study of major trauma), which uncovered 80 SNPs. <it>In silico </it>modeling was performed using Patrocles and Transcriptional Element Search System (TESS). Thirty seven novel and tagging SNPs were tested for association with ALI compared with ICU at-risk controls who did not develop ALI in a cohort study of 259 African American and 254 European American subjects that had been admitted to the ICU with major trauma.</p> <p>Results</p> <p>Resequencing of critically ill subjects demonstrated 43 novel SNPs not previously reported. Coding regions demonstrated no detectable variation, indicating conservation of the protein. Block haplotype analyses reveal that recombination rates within the gene seem low in both Caucasians and African Americans. Several novel SNPs appeared to have the potential for functional consequence using <it>in silico </it>modeling. Chi²analysis of ALI incidence and genotype showed no significant association between the SNPs in this study and ALI. Haplotype analysis did not reveal any association beyond single SNP analyses.</p> <p>Conclusions</p> <p>This study revealed novel SNPs within the <it>PRDX6 </it>gene and its 5' and 3' flanking regions via direct sequencing. There was no association found between these SNPs and ALI, possibly due to a low sample size, which was limited to detection of relative risks of 1.93 and above. Future studies may focus on the role of <it>PRDX6 </it>genetic variation in other diseases, where oxidative stress is suspected.</p

Evolution of MicroRNAs and the Diversification of Species

MicroRNAs (miRNAs) are ancient, short noncoding RNA molecules that regulate the transcriptome through post-transcriptional mechanisms. miRNA riboregulation is involved in a diverse range of biological processes, and misregulation is implicated in disease. It is generally thought that miRNAs function to canalize cellular outputs, for instance as “fail-safe” repressors of gene misexpression. Genomic surveys in humans have revealed reduced genetic polymorphism and the signature of negative selection for both miRNAs themselves and the target sequences to which they are predicted to bind. We investigated the evolution of miRNAs and their binding sites across cichlid fishes from Lake Malawi (East Africa), where hundreds of diverse species have evolved in the last million years. Using low-coverage genome sequence data, we identified 100 cichlid miRNA genes with mature regions that are highly conserved in other animal species. We computationally predicted target sites on the 3′-untranslated regions (3′-UTRs) of cichlid genes to which miRNAs may bind and found that these sites possessed elevated single nucleotide polymorphism (SNP) densities. Furthermore, polymorphic sites in predicted miRNA targets showed higher minor allele frequencies on average and greater genetic differentiation between Malawi lineages when compared with a neutral expectation and nontarget 3′-UTR SNPs. Our data suggest that divergent selection on miRNA riboregulation may have contributed to the diversification of cichlid species and may similarly play a role in rapid phenotypic evolution of other natural systems

A Cross-Species Analysis of MicroRNAs in the Developing Avian Face

Higher vertebrates use similar genetic tools to derive very different facial features. This diversity is believed to occur through temporal, spatial and species-specific changes in gene expression within cranial neural crest (NC) cells. These contribute to the facial skeleton and contain species-specific information that drives morphological variation. A few signaling molecules and transcription factors are known to play important roles in these processes, but little is known regarding the role of micro-RNAs (miRNAs). We have identified and compared all miRNAs expressed in cranial NC cells from three avian species (chicken, duck, and quail) before and after species-specific facial distinctions occur. We identified 170 differentially expressed miRNAs. These include thirty-five novel chicken orthologs of previously described miRNAs, and six avian-specific miRNAs. Five of these avian-specific miRNAs are conserved over 120 million years of avian evolution, from ratites to galliforms, and their predicted target mRNAs include many components of Wnt signaling. Previous work indicates that mRNA gene expression in NC cells is relatively static during stages when the beak acquires species-specific morphologies. However, miRNA expression is remarkably dynamic within this timeframe, suggesting that the timing of specific developmental transitions is altered in birds with different beak shapes. We evaluated one miRNA:mRNA target pair and found that the cell cycle regulator p27KIP1 is a likely target of miR-222 in frontonasal NC cells, and that the timing of this interaction correlates with the onset of phenotypic variation. Our comparative genomic approach is the first comprehensive analysis of miRNAs in the developing facial primordial, and in species-specific facial development

Regulation of antibiotic production in Actinobacteria: new perspectives from the post-genomic era

The antimicrobial activity of many of their natural products has brought prominence to the Streptomycetaceae, a family of Gram-positive bacteria that inhabit both soil and aquatic sediments. In the natural environment, antimicrobial compounds are likely to limit the growth of competitors, thereby offering a selective advantage to the producer, in particular when nutrients become limited and the developmental programme leading to spores commences. The study of the control of this secondary metabolism continues to offer insights into its integration with a complex lifecycle that takes multiple cues from the environment and primary metabolism. Such information can then be harnessed to devise laboratory screening conditions to discover compounds with new or improved clinical value. Here we provide an update of the review we published in NPR in 2011. Besides providing the essential background, we focus on recent developments in our understanding of the underlying regulatory networks, ecological triggers of natural product biosynthesis, contributions from comparative genomics and approaches to awaken the biosynthesis of otherwise silent or cryptic natural products. In addition, we highlight recent discoveries on the control of antibiotic production in other Actinobacteria, which have gained considerable attention since the start of the genomics revolution. New technologies that have the potential to produce a step change in our understanding of the regulation of secondary metabolism are also described

Evolutionary history of hoofed mammals during the Oligocene–Miocene transition in Western Europe

The biostratigraphy and diversity patterns of terrestrial, hoofed mammals help to understand the transition between the Palaeogene and the Neogene in Western Europe. Three phases are highlighted: (1) the beginning of the Arvernian (Late Oligocene, MP25-27) was characterised by a “stable” faunal composition including the last occurrences of taxa inherited from the Grande Coupure and of newly emerged ones; (2) the latest Arvernian (Late Oligocene, MP28-30) and the Agenian (Early Miocene, MN1-2) saw gradual immigrations leading to progressive replacement of the Arvernian, hoofed mammals towards the establishment of the “classical” Agenian fauna; (3) the beginning of the Orleanian (Early Miocene, MN3-4) coincided with the African-Eurasian faunal interchanges of the Proboscidean Datum Events and led to complete renewal of the Agenian taxa and total disappearance of the last Oligocene survivors. Faunal balances, poly-cohorts and particularly cluster analyses emphasise these three periods and define a temporally well-framed Oligocene–Miocene transition between MP28 and MN2. This transition started in MP28 with a major immigration event, linked to the arrival in Europe of new ungulate taxa, notably a stem group of “Eupecora” and the small anthracothere Microbunodon. Due to its high significance in the reorganisation of European, hoofed-mammal communities, we propose to name it the Microbunodon Event. This first step was followed by a phase of extinctions (MP29-30) and later by a phase of regional speciation and diversification (MN1-2). The Oligocene–Miocene faunal transition ended right before the two-phased turnover linked to the Proboscidean Datum Events (MN3-4). Locomotion types of rhinocerotids and ruminants provide new data on the evolution of environments during the Oligocene–Miocene transition and help understand the factors controlling these different phases. Indeed, it appears that the faunal turnovers were primarily directed by migrations, whereas the Agenian transitional phase mainly witnessed speciations

Trimming the complexity of Ranking by Pairwise Comparison

In computer science research, and more specifically in bioinformatics, the size of databases never stops to increase. This can be an issue when trying to answer questions that imply algorithms in nonlinear polynomial time with regards to the number of objects in the database, the number of attributes or the number of associated labels per objects. This is the case of the Ranking by Pairwise Comparison (RPC) algorithm. This algorithm builds a model which is able to predict the label preference for a given object, but the computation needs to be performed in an order of N*(N-1)/2 in terms of the number N of labels. Indeed, a pairwise comparator model is needed for each possible pair of labels. Our hypothesis is that a significant part of the set of comparators often contains redundancy and/or noise, so that trimming the set could be beneficiary. We implemented several methods, starting from the simplest one, which merely chooses a set of T comparators (T < N*(N-1)/2) at random, to a more complex approach based on partially randomized greedy search. This thesis will provide a detailed overview of the context we are working in, provide the reader with required background, describe existing preference learning algorithms including RPC, investigate on possible trimming methods and their accuracy, then will conclude on the relevance and robustness of the trimming approximation. After implementing and executing the procedure, we could see that using between N/2 and 2N comparators was sufficient to keep up with the original RPC algorithm, as long as a smart trimming method is used, and sometimes even outperforms it on noisy datasets. Also, comparing the use of base models in regression mode vs. classification mode showed that models built in regression mode may be more robust when using the original RPC. We thus empirically show that, in the particular case of RPC, reducing the complexity of the method gives similar or better results, which means that problems that could not be addressed by this algorithm, or at least not in an acceptable period of time, now can be. We also found that the regression mode yields RPC to be often more robust regarding its base learner parameters, meaning that the quest of optimality, which can also be time-consuming, is less difficult. Yet research on this topic is not over, and we could think of different means to further improve the RPC algorithm or investigate other innovative approaches, which will be discussed in the future work section. Also, the trimming method is not limited to RPC and could be applied to other algorithms which aggregate information provided by a set of models, e.g. the whole multitude of ensemble models used in machine learning

Large mammals from Rickenbach (Switzerland, reference locality MP29, Late Oligocene): biostratigraphic and palaeoenvironmental implications

Since the first exploitation of the Huppersandstones quarry of Rickenbach (Canton Solothurn, Switzerland) in 1898, many fossils of plants, molluscs, and vertebrates have been discovered. The study of the small mammals brought this locality to international recognition as the type locality for the European mammalian reference level MP29 (latest Oligocene). Our study reviews the terrestrial herbivorous mammals of Rickenbach and aims to reconstruct the palaeoenvironmental and palaeoclimatic conditions in which they lived. The perissodactyls and cetartiodactyls are described and identified: Protapirus sp. (Tapiridae), Ronzotherium romani and Diaceratherium lamilloquense (Rhinocerotidae), Anthracotherium magnum and Microbunodon minimum (Anthracotheriidae), Palaeochoerus pusillus (Suoidea), and Dremotherium guthi, “Amphitragulus” quercyi, “Amphitragulus” feningrei, and Babameryx engesseri gen. et sp. nov. (Ruminantia). Based on the updated faunal list, a cenogram of the locality of Rickenbach is established. We also performed ecomorphologic analyses on ruminants and rhinocerotids. The reconstructed palaeoenvironment of Rickenbach probably corresponded to a savannah woodland affected by a subtropical climate with clear seasonality