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  • 1
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    A novel essential domain perspective for exploring gene essentiality (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-11
    Description: Motivation: Genes with indispensable functions are identified as essential; however, the traditional gene-level studies of essentiality have several limitations. In this study, we characterized gene essentiality from a new perspective of protein domains, the independent structural or functional units of a polypeptide chain. Results: To identify such essential domains, we have developed an Expectation–Maximization (EM) algorithm-based Essential Domain Prediction (EDP) Model. With simulated datasets, the model provided convergent results given different initial values and offered accurate predictions even with noise. We then applied the EDP model to six microbial species and predicted 1879 domains to be essential in at least one species, ranging 10–23% in each species. The predicted essential domains were more conserved than either non-essential domains or essential genes. Comparing essential domains in prokaryotes and eukaryotes revealed an evolutionary distance consistent with that inferred from ribosomal RNA. When utilizing these essential domains to reproduce the annotation of essential genes, we received accurate results that suggest protein domains are more basic units for the essentiality of genes. Furthermore, we presented several examples to illustrate how the combination of essential and non-essential domains can lead to genes with divergent essentiality. In summary, we have described the first systematic analysis on gene essentiality on the level of domains. Contact: huilu.bioinfo@gmail.com or Long.Lu@cchmc.org Supplementary Information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Stable radiation pressure acceleration of ions by suppressing transverse Rayleigh-Taylor instability with multiple Gaussian pulses (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-08-05
    Description: In the case of a thin plasma slab accelerated by the radiation pressure of an ultra-intense laser pulse, the development of Rayleigh-Taylor instability (RTI) will destroy the acceleration structure and terminate the acceleration process much sooner than theoretical limit. In this paper, a new scheme using multiple Gaussian pulses for ion acceleration in a radiation pressure acceleration regime is investigated with particle-in-cell simulation. We found that with multiple Gaussian pulses, the instability could be efficiently suppressed and the divergence of the ion bunch is greatly reduced, resulting in a longer acceleration time and much more collimated ion bunch with higher energy than using a single Gaussian pulse. An analytical model is developed to describe the suppression of RTI at the laser-plasma interface. The model shows that the suppression of RTI is due to the introduction of the long wavelength mode RTI by the multiple Gaussian pulses.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Lower-Crustal Magmatic Hornblendite in North China Craton: Insight into the Genesis of Porphyry Cu Deposits (2015)
    Society of Economic Geologists (SEG)
    Details
    Publication Date: 2015-09-23
    Description: Genesis of porphyry Cu deposits remains controversial. A common view suggests that the efficient partitioning of Cu into a fluid exsolved from a calc-alkaline magma with normal Cu but elevated S concentrations is critical to ore formation. However, this view was recently challenged by two new ideas, which emphasize that the formation of porphyry Cu deposits requires anomalously Cu rich sources of either a mantle domain or intracrustal magmatic cumulate. Here we report data on an intracrustal magmatic hornblendite, genetically associated with the large Mujicun porphyry Cu deposit in North China craton. Petrographic observations, geochemical data, and P-T calculations indicate that the hornblendite formed at a depth of ~28 km by amphibole accumulation from a basaltic magma. These cumulates, despite containing traces of Cu-bearing sulfides, have Cu contents of only 17 to 60 ppm, close to primitive arc magmas. Their parental magma, initially not Cu enriched, evolved to ≥60 ppm Cu in resultant gabbronorite emplaced at ca. 8 km. This was followed by strong Cu depletion (〈10 ppm) in the quartz-diorite porphyries associated with Cu mineralization. Most of the gabbronorites contain magmatic sulfide phases that have been partially dissolved by hydrothermal fluids. One sample contains sulfide droplets and coexisting silicate glass and fluid inclusions that were locally trapped in interstitial magmatic quartz. We conclude that the exsolution of a Cu-rich sulfide melt and its subsequent redissolution into aqueous fluids was a significant factor in the formation of the Mujicun porphyry Cu deposit, and that anomalous Cu enrichments in the mantle source regime or intracrustal cumulates were not required to form the ore deposit.
    Print ISSN: 0361-0128
    Topics: Geosciences
    Published by Society of Economic Geologists (SEG)
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  • 4
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    Expanded GAA repeats impede transcription elongation through the FXN gene and induce transcriptional silencing that is restricted to the FXN locus (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-21
    Description: Friedreich's ataxia (FRDA) is a severe neurodegenerative disease caused by homozygous expansion of the guanine-adenine-adenine (GAA) repeats in intron 1 of the FXN gene leading to transcriptional repression of frataxin expression. Post-translational histone modifications that typify heterochromatin are enriched in the vicinity of the repeats, whereas active chromatin marks in this region are underrepresented in FRDA samples. Yet, the immediate effect of the expanded repeats on transcription progression through FXN and their long-range effect on the surrounding genomic context are two critical questions that remain unanswered in the molecular pathogenesis of FRDA. To address these questions, we conducted next-generation RNA sequencing of a large cohort of FRDA and control primary fibroblasts. This comprehensive analysis revealed that the GAA-induced silencing effect does not influence expression of neighboring genes upstream or downstream of FXN . Furthermore, no long-range silencing effects were detected across a large portion of chromosome 9. Additionally, results of chromatin immunoprecipitation studies confirmed that histone modifications associated with repressed transcription are confined to the FXN locus. Finally, deep sequencing of FXN pre-mRNA molecules revealed a pronounced defect in the transcription elongation rate in FRDA cells when compared with controls. These results indicate that approaches aimed to reactivate frataxin expression should simultaneously address deficits in transcription initiation and elongation at the FXN locus.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Unwinding forward and sliding back: an intermittent unwinding mode of the BLM helicase (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-21
    Description: There are lines of evidence that the Bloom syndrome helicase, BLM, catalyzes regression of stalled replication forks and disrupts displacement loops (D-loops) formed during homologous recombination (HR). Here we constructed a forked DNA with a 3' single-stranded gap and a 5' double-stranded handle to partly mimic a stalled DNA fork and used magnetic tweezers to study BLM-catalyzed unwinding of the forked DNA. We have directly observed that the BLM helicase may slide on the opposite strand for some distance after duplex unwinding at different forces. For DNA construct with a long hairpin, progressive unwinding of the hairpin is frequently interrupted by strand switching and backward sliding of the enzyme. Quantitative study of the uninterrupted unwinding length (time) has revealed a two-state-transition mechanism for strand-switching during the unwinding process. Mutational studies revealed that the RQC domain plays an important role in stabilizing the helicase/DNA interaction during both DNA unwinding and backward sliding of BLM. Especially, Lys1125 in the RQC domain, a highly conserved amino acid among RecQ helicases, may be involved in the backward sliding activity. We have also directly observed the in vitro pathway that BLM disrupts the mimic stalled replication fork. These results may shed new light on the mechanisms for BLM in DNA repair and homologous recombination.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Earth's Bow Shock: A New Three‐Dimensional Asymmetric Model With Dipole Tilt Effects (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract Using the bow shock crossing events from four spacecraft: IMP 8, Geotail, Magion‐4, and Cluster 1, a new three‐dimensional asymmetric bow shock model is constructed. The model is parameterized by the solar wind dynamic pressure, the interplanetary magnetic field, magnetosonic Mach number, solar wind β, and the Earth's dipole tilt angle. It is shown that the shape and size of bow shock are both affected by the dipole tilt angle. The dipole tilt angle causes asymmetries in the meridional plane: (1) the bow shock subsolar standoff distance and the north‐south asymmetry increase with the dipole tilt angle; (2) as the dipole tilt angle increases, the shock flaring angle in the equatorial plane is slightly reduced, while in the meridional plane the flaring angle obviously decreases in Southern Hemisphere and keeps almost unchanged in the Northern Hemisphere. The flaring angle in the Northern Hemisphere is larger than in the Southern Hemisphere; (3) the effects of negative dipole tilt angle on shock flaring are just the opposite of those for positive tilt, and the effects of dipole tilt angle on the shape of the bow shock are north‐south symmetric. The model results are also validated by comparing with one previous empirical model and with observational crossings, and it is demonstrated that the new model is able to predict the observed crossings more accurately and can better describe the rotational asymmetry and north‐south asymmetry of the Earth's bow shock.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
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    The inferred evolution of the cold gas properties of CANDELS galaxies at 0.5 〈 z 〈 3.0 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-15
    Description: We derive the total cold gas, atomic hydrogen, and molecular gas masses of approximately 24 000 galaxies covering four decades in stellar mass at redshifts 0.5 〈 z 〈 3.0, taken from the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey survey. Our inferences are based on the inversion of a molecular hydrogen based star formation law, coupled with a prescription to separate atomic and molecular gas. We find that: (1) there is an increasing trend between the inferred cold gas (H i and H 2 ), H i , and H 2 mass and the stellar mass of galaxies down to stellar masses of 10 8 M already in place at z = 3; (2) the molecular fractions of cold gas increase with increasing stellar mass and look-back time; (3) there is hardly any evolution in the mean H i content of galaxies at fixed stellar mass; (4) the cold gas fraction and relative amount of molecular hydrogen in galaxies decrease at a relatively constant rate with time, independent of stellar mass; (5) there is a large population of low stellar mass galaxies dominated by atomic gas. These galaxies are very gas rich, but only a minor fraction of their gas is molecular; 6) the ratio between star formation rate (SFR) and inferred total cold gas mass (H i + H 2 ) of galaxies (i.e. star formation efficiency; SFE) increases with star formation at fixed stellar masses. Due to its simplicity, the presented approach is valuable to assess the impact of selection biases on small samples of directly observed gas masses and to extend scaling relations down to stellar mass ranges and redshifts that are currently difficult to probe with direct measurements of gas content.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Spin I ground state probabilities of integrable systems under random interactions (2015)
    American Physical Society (APS)
    Details
    Publication Date: 2015-02-10
    Description: Author(s): Y. Lu, Y. M. Zhao, and A. Arima In this paper we revisit spin I ground state probabilities (denoted by P(I)) of a few integrable systems under random interactions. We obtain explicit and simple formulas of P(I) for d-boson systems and fermions in a j=5/2 shell. [Phys. Rev. C 91, 027301] Published Mon Feb 09, 2015
    Keywords: Nuclear Structure
    Print ISSN: 0556-2813
    Electronic ISSN: 1089-490X
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Solids Holdup of High Flux Circulating Fluidized Bed at Elevated Pressure (2012)
    Wiley
    Details
    Publication Date: 2012-04-05
    Description: Experimental studies on the solids holdup of a high-flux circulating fluidized bed (HFCFB) at an operating pressure up to 0.5 MPa were carried out. The effects of operating pressure, solids mass flux and superficial gas velocity on the solids holdup distribution were systematically tested. It was found that the solids holdup at elevated pressure increases with increasing solids mass flux but decreases with increasing superficial gas velocity, which is similar to the trends at atmospheric condition. As a result, the condition of a high-density circulating fluidized bed (HDCFB), i.e., solids holdup in everywhere of the riser is larger than 10 %) is easier to be achieved at elevated pressure than in a HDCFB operated at atmospheric pressure. In the current work, the condition of a full HDCFB with Geldart group B particles has been achieved successfully at 0.5 MPa. Experiments on the flow behavior in a high-flux circulating fluidized bed with Geldart group B particles were carried out at various operating pressures, solids mass fluxes and standard state superficial gas velocities. The influence of operating pressure, solids mass flux and superficial gas velocity on the solids holdup distribution were systematically tested.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 10
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    Solids Holdup of High Flux Circulating Fluidized Bed at Elevated Pressure (2012)
    Wiley
    Details
    Publication Date: 2012-04-15
    Description: Experimental studies on the solids holdup of a high-flux circulating fluidized bed (HFCFB) at an operating pressure up to 0.5 MPa were carried out. The effects of operating pressure, solids mass flux and superficial gas velocity on the solids holdup distribution were systematically tested. It was found that the solids holdup at elevated pressure increases with increasing solids mass flux but decreases with increasing superficial gas velocity, which is similar to the trends at atmospheric condition. As a result, the condition of a high-density circulating fluidized bed (HDCFB), i.e., solids holdup in everywhere of the riser is larger than 10 %) is easier to be achieved at elevated pressure than in a HDCFB operated at atmospheric pressure. In the current work, the condition of a full HDCFB with Geldart group B particles has been achieved successfully at 0.5 MPa. Experiments on the flow behavior in a high-flux circulating fluidized bed with Geldart group B particles were carried out at various operating pressures, solids mass fluxes and standard state superficial gas velocities. The influence of operating pressure, solids mass flux and superficial gas velocity on the solids holdup distribution were systematically tested.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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