Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Background: Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the Drosophila RNA-binding Bruno-3 (Bru-3) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results: Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion: We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution

Implications on Inelastic Dark Matter from 100 Live Days of XENON100 Data

The XENON100 experiment has recently completed a dark matter run with 100.9 live-days of data, taken from January to June 2010. Events in a 48kg fiducial volume in the energy range between 8.4 and 44.6 keVnr have been analyzed. A total of three events have been found in the predefined signal region, compatible with the background prediction of (1.8 \pm 0.6) events. Based on this analysis we present limits on the WIMP-nucleon cross section for inelastic dark matter. With the present data we are able to rule out the explanation for the observed DAMA/LIBRA modulation as being due to inelastic dark matter scattering off iodine at a 90% confidence level.Comment: 3 pages, 3 figure

Multi-mode ultra-strong coupling in circuit quantum electrodynamics

With the introduction of superconducting circuits into the field of quantum optics, many novel experimental demonstrations of the quantum physics of an artificial atom coupled to a single-mode light field have been realized. Engineering such quantum systems offers the opportunity to explore extreme regimes of light-matter interaction that are inaccessible with natural systems. For instance the coupling strength $g$ can be increased until it is comparable with the atomic or mode frequency $\omega_{a,m}$ and the atom can be coupled to multiple modes which has always challenged our understanding of light-matter interaction. Here, we experimentally realize the first Transmon qubit in the ultra-strong coupling regime, reaching coupling ratios of $g/\omega_{m}=0.19$ and we measure multi-mode interactions through a hybridization of the qubit up to the fifth mode of the resonator. This is enabled by a qubit with 88% of its capacitance formed by a vacuum-gap capacitance with the center conductor of a coplanar waveguide resonator. In addition to potential applications in quantum information technologies due to its small size and localization of electric fields in vacuum, this new architecture offers the potential to further explore the novel regime of multi-mode ultra-strong coupling.Comment: 15 pages, 9 figure

Spartan Daily, April 25, 1949

Volume 37, Issue 119https://scholarworks.sjsu.edu/spartandaily/11232/thumbnail.jp

Dark Matter Results from 100 Live Days of XENON100 Data

We present results from the direct search for dark matter with the XENON100 detector, installed underground at the Laboratori Nazionali del Gran Sasso of INFN, Italy. XENON100 is a two-phase time projection chamber with a 62 kg liquid xenon target. Interaction vertex reconstruction in three dimensions with millimeter precision allows to select only the innermost 48 kg as ultra-low background fiducial target. In 100.9 live days of data, acquired between January and June 2010, no evidence for dark matter is found. Three candidate events were observed in a pre-defined signal region with an expected background of 1.8 +/- 0.6 events. This leads to the most stringent limit on dark matter interactions today, excluding spin-independent elastic WIMP-nucleon scattering cross-sections above 7.0x10^-45 cm^2 for a WIMP mass of 50 GeV/c^2 at 90% confidence level.Comment: 5 pages, 5 figures; matches accepted versio

Persistent systemic microbial translocation, inflammation, and intestinal damage during Clostridioides difficile infection

Background. Clostridioides difficile infection (CDI) might be complicated by the development of nosocomial bloodstream infection (n-BSI). Based on the hypothesis that alteration of the normal gut integrity is present during CDI, we evaluated markers of microbial translocation, inflammation, and intestinal damage in patients with CDI. Methods. Patients with documented CDI were enrolled in the study. For each subject, plasma samples were collected at T0 and T1 (before and after CDI therapy, respectively), and the following markers were evaluated: lipopolysaccharide-binding protein (LPB), EndoCab IgM, interleukin-6, intestinal fatty acid binding protein (I-FABP). Samples from nonhospitalized healthy controls were also included. The study population was divided into BSI+/BSI- and fecal microbiota transplantation (FMT) +/FMT- groups, according to the development of n-BSI and the receipt of FMT, respectively. Results. Overall, 45 subjects were included; 8 (17.7%) developed primary n-BSI. Markers of microbial translocation and intestinal damage significantly decreased between T0 and T1, however, without reaching values similar to controls (P < .0001). Compared with BSI-, a persistent high level of microbial translocation in the BSI+ group was observed. In the FMT+ group, markers of microbial translocation and inflammation at T1 tended to reach control values. Conclusions. CDI is associated with high levels of microbial translocation, inflammation, and intestinal damage, which are still present at clinical resolution of CDI. The role of residual mucosal perturbation and persistence of intestinal cell damage in the development of n-BSI following CDI, as well as the possible effect of FMT in the restoration of mucosal integrity, should be further investigated

Effects of short-range order on the electronic structure of disordered metallic systems

For many years the Korringa-Kohn-Rostoker coherent-potential approximation (KKR-CPA) has been widely used to describe the electronic structure of disordered systems based upon a first-principles description of the crystal potential. However, as a single-site theory the KKR-CPA is unable to account for important environmental effects such as short-range order (SRO) in alloys and spin fluctuations in magnets, amongst others. Using the recently devised KKR-NLCPA (where NL stands for nonlocal), we show how to remedy this by presenting explicit calculations for the effects of SRO on the electronic structure of the bcc Cu_{50}Zn_{50} solid solution.Comment: 8 pages, 6 figures, Revised versio