ALBERT

Description: Gene fusions and their products (RNA and protein) were once thought to be unique features to cancer. However, chimeric RNAs can also be found in normal cells. Here, we performed, curated and analyzed nearly 300 RNA-Seq libraries covering 30 different non-neoplastic human tissues and cells as well as 15 mouse tissues. A large number of fusion transcripts were found. Most fusions were detected only once, while 291 were seen in more than one sample. We focused on the recurrent fusions and performed RNA and protein level validations on a subset. We characterized these fusions based on various features of the fusions, and their parental genes. They tend to be expressed at higher levels relative to their parental genes than the non-recurrent ones. Over half of the recurrent fusions involve neighboring genes transcribing in the same direction. A few sequence motifs were found enriched close to the fusion junction sites. We performed functional analyses on a few widely expressed fusions, and found that silencing them resulted in dramatic reduction in normal cell growth and/or motility. Most chimeras use canonical splicing sites, thus are likely products of ‘intergenic splicing’. We also explored the implications of these non-pathological fusions in cancer and in evolution.

Description: Motivation: By capturing various biochemical interactions, biological pathways provide insight into underlying biological processes. Given high-dimensional microarray or RNA-sequencing data, a critical challenge is how to integrate them with rich information from pathway databases to jointly select relevant pathways and genes for phenotype prediction or disease prognosis. Addressing this challenge can help us deepen biological understanding of phenotypes and diseases from a systems perspective. Results: In this article, we propose a novel sparse Bayesian model for joint network and node selection. This model integrates information from networks (e.g. pathways) and nodes (e.g. genes) by a hybrid of conditional and generative components. For the conditional component, we propose a sparse prior based on graph Laplacian matrices, each of which encodes detailed correlation structures between network nodes. For the generative component, we use a spike and slab prior over network nodes. The integration of these two components, coupled with efficient variational inference, enables the selection of networks as well as correlated network nodes in the selected networks. Simulation results demonstrate improved predictive performance and selection accuracy of our method over alternative methods. Based on three expression datasets for cancer study and the KEGG pathway database, we selected relevant genes and pathways, many of which are supported by biological literature. In addition to pathway analysis, our method is expected to have a wide range of applications in selecting relevant groups of correlated high-dimensional biomarkers. Availability: The code can be downloaded at www.cs.purdue.edu/homes/szhe/software.html . Contact: alanqi@purdue.edu

Description: A mechanically formed electrical nanocontact between gold and tungsten is a prototypical junction between metals with dissimilar electronic structure. Through atomically characterized nanoindentation experiments and first-principles quantum transport calculations, we find that the ballistic conduction across this intermetallic interface is drastically reduced because of the fundamental mismatch between s wave-like...

Description: Staphylococcal protein A (SpA) is an important virulence factor from Staphylococcus aureus responsible for the bacterium’s evasion of the host immune system. SpA includes five small three-helix–bundle domains that can each bind with high affinity to many host proteins such as antibodies. The interaction between a SpA domain and the...

Description: In this experiment, white seed pumpkin ‘Shengzhen No. 1’ was used as rootstock for the oriental sweet melon ( Cucumis melo L. ) ‘Yumeiren’. The fruits of own-rooted melons were used as control. The objective of this experiment was to study the effects of grafting on the following parameters: content of free fatty acids and activities of synthetic enzymes (LOX, ADH, and AAT). These parameters were measured in the peel and flesh tissues of oriental sweet melon at different time-points. Due to grafting, the content of oleic acid and linolenic acid decreased in peel tissues of melons at early stages of maturity. Therefore, total contents of free fatty acids were lower than those of control. However, there was no significant difference in the content of three free fatty acids in flesh tissue; this content was lower than that in peel tissue. Due to grafting, enzymatic activities of ADH and AAT decreased in peel tissue of melons; however, these enzymes showed different activities ...

Description: The properties of bound-bound transitions in hydrogen-like ions in dense quantum plasmas, characterized by a cosine-Debye-Hückel interaction between charged particles, are studied in detail. The transition frequencies, oscillator strengths, and radiative transition probabilities of Lyman and Balmer series are calculated for a wide range of screening strengths of the interaction up to the n  = 5 shell. For Δ n ≠ 0 transitions, all these quantities exhibit a significant decrease with increasing screening strength, while for the Δ n = 0 transitions and for the radiative lifetimes, the opposite is true. The present results are compared with those available from the literature. They are also compared with the results for the pure Debye-Hückel potential with the same screening strength.

Description: Author(s): Y. Qi, J. M. P. Martirez, Wissam A. Saidi, J. J. Urban, W. S. Yun, J. E. Spanier, and A. M. Rappe We investigate the origin of the depolarization rates in ultrathin adsorbate-stabilized ferroelectric wires. By applying density functional theory calculations and analytic modeling, we demonstrate that the depolarization results from the leakage of charges stored at the surface adsorbates, which pl… [Phys. Rev. B 91, 245431] Published Wed Jun 24, 2015

Description: Many studies have aimed to set up boundaries for the classification and definition of prokaryotic genus and species classification; however, studies that focused on genus-level genomic differences for existing taxonomy systems are limited. Recently, a novel method was described for prokaryotic genus delineation using the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance (Qin et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196 :2210–5). Here, we extended the POCP analysis of the order Chlamydiales and pairwise compared all currently recognized species and candidate species of the family Chlamydiaceae as well as some species from other families. Using the taxonomy advised by the International Committee on Systematics of Prokaryotes, subcommittee on the taxonomy of the Chlamydiae , POCP analysis revealed that all pairwise comparisons of species from different families resulted in values lower than 50%, the proposed threshold for genus boundary. In contrast, all interspecies pairwise comparisons of species from the single genus within the family Chlamydiaceae resulted in POCP values higher than 70%. We conclude that the recommended genus classification of the family Chlamydiaceae is rational and that POCP analyses can provide a robust genomic index for the taxonomy of members of the order Chlamydiales in terms of genus demarcation.

Description: The Poyi magmatic Ni-Cu sulfide deposit is situated in the Beishan fold belt in the northeastern rim of the Tarim craton. Many Permian magmatic Ni-Cu sulfide deposits, such as those in East Tianshan, are present in the adjacent Central Asian orogenic belt to the north. The Poyi deposit is hosted in a small dike-like ultramafic-troctolitic body that was emplaced into a much larger gabbroic intrusion. Our new zircon U-Pb isotope data reveal that these two intrusions formed ~6 Ma apart. The ultramafic-troctolitic intrusion was emplaced at 269.9 ± 1.7 Ma, whereas the gabbroic intrusion was emplaced at 276.1 ± 1.9 Ma. The results show that the Poyi deposit is the youngest among the major magmatic Ni-Cu sulfide deposits (≥0.2 Mt Ni) of Permian ages in the Beishan-Tianshan region. Sulfide mineralization in the Poyi deposit occurs as steeply dipping disseminated sulfide lenses mostly associated with wehrlites in the center of the dike. Olivine from the Poyi ultramafic rocks has Fo content up to 91 mol %, which is similar to the lower limit of mantle olivine and the most primitive within the Permian Beishan-Tianshan nickel belt. Like other magmatic sulfide deposits in this belt, olivine from the Poyi deposit is depleted in Ca (〈1,000 ppm). The estimated parental magma for the Poyi most primitive ultramafic rocks contains 15 ± 2 wt % MgO. Cotectic olivine-sulfide segregation from the Poyi magma is inferred from systematic variation of Fo-Ni contents in olivine from some sulfide-barren ultramafic rock samples, and supported by the occurrence of sulfide droplets as small inclusions in olivine (Fo 90 mol %) in these rocks. The involvement of multiple pulses of sulfide-charged magma with different compositions is indicated by the abrupt change of olivine Fo content with depth and the presence of olivine with similar Fo contents but dramatically different Ni abundances in the different parts of the deposit. The ( 87 Sr/ 86 Sr) i ratios and Nd(total) of the Poyi ultramafic rocks and troctolites range from 0.7042 to 0.7052 and from 4.9 to 6.0, respectively, which are close to the isotope compositions of depleted mantle and within the ranges of major magmatic Ni-Cu sulfide deposits of Permian ages in East Tianshan. No more than 5 wt % of bulk crustal contamination is required to explain the variations of Sr-Nd isotopes in the Poyi ultramafic-troctolitic intrusion. The abundances of incompatible trace elements in whole rocks and clinopyroxene crystals indicate very weak light REE enrichments coupled by significant negative Nb-Ta anomalies in the parental melts. Bulk sulfides in the Poyi deposit are characterized by positive correlations between any pair of platinum-group elements (PGE), indicating that PGE tenor variations in the deposit are mainly controlled by variable R-factors (magma/sulfide mass ratios). The estimated initial concentrations of PGE in the parental magma for the Poyi deposit are almost two orders of magnitude lower than the abundances of PGE in some continental picrites. Given that the parental magma for the Poyi deposit is as primitive as a primary mantle-derived magma, the depletion of PGE in the Poyi deposit is most likely due to previous sulfide segregation at depth. Based on these observations, we conclude that sulfide saturation in the Poyi PGE-depleted, Mg-rich magma was triggered by addition of crustal sulfur during magma ascent and that the Poyi deposit was a dynamic conduit used by multiple pulses of olivine- and sulfide-charged magma.

Description: Starved animals often exhibit elevated locomotion, which has been speculated to partly resemble foraging behavior and facilitate food acquisition and energy intake. Despite its importance, the neural mechanism underlying this behavior remains unknown in any species. In this study we confirmed and extended previous findings that starvation induced locomotor activity...