CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24–47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature of the spacers are often quite diverse, even among strains of a same species. Furthermore, the acquisition of new units (DR + spacer) was shown to happen almost exclusively on one side of the locus. Therefore, the CRISPR presents an interesting genetic marker for comparative and evolutionary analysis of closely related bacterial strains. CRISPRcompar is a web service created to assist biologists in the CRISPR typing process. Two tools facilitates the in silico investigation: CRISPRcomparison and CRISPRtionary. This website is freely accessible at http://crispr.u-psud.fr/CRISPRcompar/

PILER-CR: Fast and accurate identification of CRISPR repeats

BACKGROUND: Sequencing of prokaryotic genomes has recently revealed the presence of CRISPR elements: short, highly conserved repeats separated by unique sequences of similar length. The distinctive sequence signature of CRISPR repeats can be found using general-purpose repeat- or pattern-finding software tools. However, the output of such tools is not always ideal for studying these repeats, and significant effort is sometimes needed to build additional tools and perform manual analysis of the output. RESULTS: We present PILER-CR, a program specifically designed for the identification and analysis of CRISPR repeats. The program executes rapidly, completing a 5 Mb genome in around 5 seconds on a current desktop computer. We validate the algorithm by manual curation and by comparison with published surveys of these repeats, finding that PILER-CR has both high sensitivity and high specificity. We also present a catalogue of putative CRISPR repeats identified in a comprehensive analysis of 346 prokaryotic genomes. CONCLUSION: PILER-CR is a useful tool for rapid identification and classification of CRISPR repeats. The software is donated to the public domain. Source code and a Linux binary are freely available at

The New Horizons Spacecraft

The New Horizons spacecraft was launched on 19 January 2006. The spacecraft was designed to provide a platform for seven instruments that will collect and return data from Pluto in 2015. The design drew on heritage from previous missions developed at The Johns Hopkins University Applied Physics Laboratory (APL) and other missions such as Ulysses. The trajectory design imposed constraints on mass and structural strength to meet the high launch acceleration needed to reach the Pluto system prior to the year 2020. The spacecraft subsystems were designed to meet tight mass and power allocations, yet provide the necessary control and data handling finesse to support data collection and return when the one-way light time during the Pluto flyby is 4.5 hours. Missions to the outer solar system require a radioisotope thermoelectric generator (RTG) to supply electrical power, and a single RTG is used by New Horizons. To accommodate this constraint, the spacecraft electronics were designed to operate on less than 200 W. The spacecraft system architecture provides sufficient redundancy to provide a probability of mission success of greater than 0.85, even with a mission duration of over 10 years. The spacecraft is now on its way to Pluto, with an arrival date of 14 July 2015. Initial inflight tests have verified that the spacecraft will meet the design requirements.Comment: 33 pages, 13 figures, 4 tables; To appear in a special volume of Space Science Reviews on the New Horizons missio

The Ursinus Weekly, December 2, 1968

Arts Forum held; 4 foreign students featured on panel • Board OKs student members on committees; Student Senate endorses SFARC resolution • Camino real scheduled for December 6th • Mandrake concert is hit; Rock group shows profit • Editorial: Our play; The larger issue • Letters to the editor • Tradition vs. change • Herberg sees anomic moral crisis; Fun morality termed other directed • SFARC minutes • Opinion: Speaker fails to prove dilemma • Freeland Hall: Don\u27t let it be forgot • Senior looks at Freeland: Can Library replace Freeland\u27s primacy? • Search into history substantiates claim of second oldest graduate that Freeland was everything • Instructor asks what do students really want? • Now is the time to unite • WRUC increases wattage to allow greater service • USGA discusses Black Alliance • Students to decide on two government proposals • Pratt art show opens at Ursinus • PNE Folk Fest held; U.C. talent featured • U.C. sponsors Career Days • Howard honored for achievements • Gurzynski\u27s men win title; Albert leads UC to championship • Soccer team edges LaSalle after losing to Haverford • Flowers win intramural crown with 6-0 victory over Sig Rho • Whatley lauds squad; predicts progress • Bears destroy Haverford; Shuman wins Maxwell Award • All Stars will visit Glassboro • Greek gleaningshttps://digitalcommons.ursinus.edu/weekly/1167/thumbnail.jp

Acoustic measurements in the collimation region of the LHC

The LHC accelerator at CERN has the most advanced collimation system ever being installed. The collimators intercept unavoidable particle losses and therefore are essential to avoid beam induced quenches of the superconducting magnets. In addition, they provide passive machine protection against mis-kicked beams. During material robustness tests on a LHC collimator prototype in 2004 and 2006, vibration and acoustic measurements have shown that a beam impact detection system should be feasible using accelerometers and microphones as sensors in the LHC. Recently, such sensors have been installed close to the primary collimators in the LHC tunnel. First analyses of raw data show that the system is sensitive enough to detect beam scraping on collimators. Therefore, the implementation of a sophisticated acoustic monitoring system is under investigation. It may be useful not only to detect beam impacts on primary collimators in case of failure, but also to derive further information on beam losses that occur during regular operation. This paper gives an overview on the recent installation, results of the acoustic measurements made at the LHC, and future plans.peer-reviewe

Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?

The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. The relationship of the Pseudomonas genus to Azotobacter vinelandii is examined using three genomic sequence-based methods. First, using 16S rRNA trees, it is shown that A. vinelandii groups within the Pseudomonas close to Pseudomonas aeruginosa. Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster. Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms. Third, exhaustive BLAST comparisons demonstrate that the fraction of shared genes between A. vinelandii and Pseudomonas genomes is similar to that of Pseudomonas species with each other. The results of these different methods point to a high similarity between A. vinelandii and the Pseudomonas genus, suggesting that Azotobacter might actually be a Pseudomonas

Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: A Streamlined Genome Overrun by Mobile Genetic Elements

The complete sequence of the 1,267,782 bp genome of Wolbachia pipientis wMel, an obligate intracellular bacteria of Drosophila melanogaster, has been determined. Wolbachia, which are found in a variety of invertebrate species, are of great interest due to their diverse interactions with different hosts, which range from many forms of reproductive parasitism to mutualistic symbioses. Analysis of the wMel genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights into the biology and evolution of wMel and Wolbachia in general. For example, the wMel genome is unique among sequenced obligate intracellular species in both being highly streamlined and containing very high levels of repetitive DNA and mobile DNA elements. This observation, coupled with multiple evolutionary reconstructions, suggests that natural selection is somewhat inefficient in wMel, most likely owing to the occurrence of repeated population bottlenecks. Genome analysis predicts many metabolic differences with the closely related Rickettsia species, including the presence of intact glycolysis and purine synthesis, which may compensate for an inability to obtain ATP directly from its host, as Rickettsia can. Other discoveries include the apparent inability of wMel to synthesize lipopolysaccharide and the presence of the most genes encoding proteins with ankyrin repeat domains of any prokaryotic genome yet sequenced. Despite the ability of wMel to infect the germline of its host, we find no evidence for either recent lateral gene transfer between wMel and D. melanogaster or older transfers between Wolbachia and any host. Evolutionary analysis further supports the hypothesis that mitochondria share a common ancestor with the α-Proteobacteria, but shows little support for the grouping of mitochondria with species in the order Rickettsiales. With the availability of the complete genomes of both species and excellent genetic tools for the host, the wMel–D. melanogaster symbiosis is now an ideal system for studying the biology and evolution of Wolbachia infections

The structural plasticity of white matter networks following anterior temporal lobe resection

Anterior temporal lobe resection is an effective treatment for refractory temporal lobe epilepsy. The structural consequences of such surgery in the white matter, and how these relate to language function after surgery remain unknown. We carried out a longitudinal study with diffusion tensor imaging in 26 left and 20 right temporal lobe epilepsy patients before and a mean of 4.5 months after anterior temporal lobe resection. The whole-brain analysis technique tract-based spatial statistics was used to compare pre- and postoperative data in the left and right temporal lobe epilepsy groups separately. We observed widespread, significant, mean 7%, decreases in fractional anisotropy in white matter networks connected to the area of resection, following both left and right temporal lobe resections. However, we also observed a widespread, mean 8%, increase in fractional anisotropy after left anterior temporal lobe resection in the ipsilateral external capsule and posterior limb of the internal capsule, and corona radiata. These findings were confirmed on analysis of the native clusters and hand drawn regions of interest. Postoperative tractography seeded from this area suggests that this cluster is part of the ventro-medial language network. The mean pre- and postoperative fractional anisotropy and parallel diffusivity in this cluster were significantly correlated with postoperative verbal fluency and naming test scores. In addition, the percentage change in parallel diffusivity in this cluster was correlated with the percentage change in verbal fluency after anterior temporal lobe resection, such that the bigger the increase in parallel diffusivity, the smaller the fall in language proficiency after surgery. We suggest that the findings of increased fractional anisotropy in this ventro-medial language network represent structural reorganization in response to the anterior temporal lobe resection, which may damage the more susceptible dorso-lateral language pathway. These findings have important implications for our understanding of brain injury and rehabilitation, and may also prove useful in the prediction and minimization of postoperative language deficits

Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations

Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors