Automated FingerPrint Background removal: FPB

<p>Abstract</p> <p>Background</p> <p>The construction of a whole-genome physical map has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project. Its usefulness has been proved for whole-genome shotgun projects as a post-assembly validation and recently it has also been used in the assembly step to constrain on BACs positions. Fingerprinting is usually the method of choice for construction of physical maps. A clone fingerprint is composed of true peaks representing real fragments and background peaks, mainly composed of <it>E. coli </it>genomic DNA, partial digestions, star activity by-products, and machine background. High-throughput fingerprinting leads to the production of thousands of BAC clone fingerprints per day. That is why background peaks removal has become an important issue and needs to be automatized, especially in capillary electrophoresis based fingerprints.</p> <p>Results</p> <p>At the moment, the only tools available for such a task are <it>GenoProfiler </it>and its descendant <it>FPMiner</it>. The large variation in the quality of fingerprints that is usually present in large fingerprinting projects represents a major difficulty in the correct removal of background peaks that has only been partially addressed by the methods so far adopted that all require a long manual optimization of parameters. Thus, we implemented a new data-independent tool, <it>FPB </it>(FingerPrint Background removal), suitable for large scale projects as well as mapping of few clones.</p> <p>Conclusion</p> <p><it>FPB </it>is freely available at <url>http://www.appliedgenomics.org/tools.php</url>. <it>FPB </it>was used to remove the background from all fingerprints of three grapevine physical map projects. The first project consists of about 50,000 fingerprints, the second one consists of about 70,000 fingerprints, and the third one consists of about 45,000 fingerprints. In all cases a successful assembly was built.</p

Light-Induced Charge Accumulation in PTCDI/Pentacene/Ag(111) Heterojunctions

The incorporation of singlet fission (SF) chromophores in solar cells is expected to bring significant increases in the power conversion efficiency thanks to multiexciton generation. However, efficient charge generation in the device is determined by the energy level alignment (ELA) between the active materials, which should favor exciton transport and separation under illumination. By combining ultraviolet photoemission spectroscopy and optical differential reflectance measurements, we determine the ELA in a prototypical SF heterojunction between pentacene (Pc) and perylene-tetracarboxylic-diimide (PTCDI) grown on Ag(111). Time-resolved X-ray photoelectron spectroscopy on such a system reveals light-induced modifications of the ELA; by measuring the transient shift of the core level photoemission lines we observe an accumulation of long-lived holes in the PTCDI within the first hundred picoseconds after the optical pump

Galectin-3. One molecule for an alphabet of diseases, from A to Z

Galectin-3 (Gal-3) regulates basic cellular functions such as cell–cell and cell–matrix interactions, growth, proliferation, differentiation, and inflammation. It is not surprising, therefore, that this protein is involved in the pathogenesis of many relevant human diseases, including cancer, fibrosis, chronic inflammation and scarring affecting many different tissues. The papers published in the literature have progressively increased in number during the last decades, testifying the great interest given to this protein by numerous researchers involved in many different clinical contexts. Considering the crucial role exerted by Gal-3 in many different clinical conditions, Gal-3 is emerging as a new diagnostic, prognostic biomarker and as a new promising therapeutic target. The current review aims to extensively examine the studies published so far on the role of Gal-3 in all the clinical conditions and diseases, listed in alphabetical order, where it was analyzed

Making ARPES Measurements on Corrugated Monolayer Crystals: Suspended Exfoliated Single-Crystal Graphene

Free-standing exfoliated monolayer graphene is an ultra-thin flexible membrane, which exhibits out of plane deformation or corrugation. In this paper, a technique is described to measure the band structure of such free-standing graphene by angle-resolved photoemission. Our results show that photoelectron coherence is limited by the crystal corrugation. However, by combining surface morphology measurements of the graphene roughness with angle-resolved photoemission, energy dependent quasiparticle lifetime and bandstructure measurements can be extracted. Our measurements rely on our development of an analytical formulation for relating the crystal corrugation to the photoemission linewidth. Our ARPES measurements show that, despite significant deviation from planarity of the crystal, the electronic structure of exfoliated suspended graphene is nearly that of ideal, undoped graphene; we measure the Dirac point to be within 25 meV of $E_F$ . Further, we show that suspended graphene behaves as a marginal Fermi-liquid, with a quasiparticle lifetime which scales as $(E - E_F)^{-1}$; comparison with other graphene and graphite data is discussed

ultrafast electron injection into photo excited organic molecules

State-of-the-art X-ray spectroscopy allows femtosecond gating of energy levels of photo-excited molecules on a metal substrate enabling ultrafast and bi-directional charge transfer across the interface with controllable dependence on the molecular adsorption geometry

Morphological modulation of graphene-mediated hybridization in plasmonic systems

Graphene laid on plasmonic Au-nanoparticle arrays becomes uniaxially wrinkled and induces optical anisotropy in the plasmonic response of the system

Correction: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

The version of this article published in BMC Genomics 2009, 10:558, contains data in Table 1 which are now known to be unreliable, and an illustration, in Figure 1, of unusual miRNA processing events predicted by these unreliable data. In this full-length correction, new data replace those found to be unreliable, leading to a more straightforward interpretation without altering the principle conclusions of the study. Table 1 and associated methods have been corrected, Figure 1 deleted, supplementary file 1 added, and modifications made to the sections "Deep sequencing of small RNAs from grapevine leaf tissue" and "Microarray analysis of miRNA expression". The editors and authors regret the inconvenience caused to readers by premature publication of the original paper

High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are short (~21 base) single stranded RNAs that, in plants, are generally coded by specific genes and cleaved specifically from hairpin precursors. MicroRNAs are critical for the regulation of multiple developmental, stress related and other physiological processes in plants. The recent annotation of the genome of the grapevine (<it>Vitis vinifera </it>L.) allowed the identification of many putative conserved microRNA precursors, grouped into multiple gene families.</p> <p>Results</p> <p>Here we use oligonucleotide arrays to provide the first indication that many of these microRNAs show differential expression patterns between tissues and during the maturation of fruit in the grapevine. Furthermore we demonstrate that whole transcriptome sequencing and deep-sequencing of small RNA fractions can be used both to identify which microRNA precursors are expressed in different tissues and to estimate genomic coordinates and patterns of splicing and alternative splicing for many primary miRNA transcripts.</p> <p>Conclusion</p> <p>Our results show that many microRNAs are differentially expressed in different tissues and during fruit maturation in the grapevine. Furthermore, the demonstration that whole transcriptome sequencing can be used to identify candidate splicing events and approximate primary microRNA transcript coordinates represents a significant step towards the large-scale elucidation of mechanisms regulating the expression of microRNAs at the transcriptional and post-transcriptional levels.</p