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  • 1
    Publication Date: 2013-01-03
    Description: [1]  CMIP5 multimodel ensemble projection of midlatitude storm track changes has been examined. Storm track activity is quantified by temporal variance of meridional wind and sea level pressure (psl), as well as cyclone track statistics. For the Southern Hemisphere (SH), CMIP5 models project clear poleward migration, upward expansion, and intensification of the storm track. For the Northern Hemisphere (NH), the models also project some poleward shift and upward expansion of the storm track in the upper troposphere/lower stratosphere, but mainly weakening of the storm track toward its equatorward flank in the troposphere. Consistent with these, CMIP5 models project significant increase in the frequency of extreme cyclones during the SH cool season, but significant decrease in such events in the NH. Comparisons with CMIP3 projections indicate high degrees of consistency for SH projections, but significant differences are found in the NH. Overall, CMIP5 models project larger decrease in storm track activity in the NH troposphere, especially over North America in winter, where psl variance as well as cyclone frequency and amplitude are all projected to decrease significantly. In terms of climatology, similar to CMIP3, most CMIP5 models simulate storm tracks that are too weak and display equatorward biases in their latitude. These biases have also been related to future projections. In the NH, the strength of a model's climatological storm track is negatively correlated with its projected amplitude change under global warming, while in the SH, models with large equatorward biases in storm track latitude tend to project larger poleward shifts.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
    Publication Date: 2012-07-22
    Description: During V(D)J recombination, the RAG1/2 recombinase is thought to play an active role in transferring newly excised recombination ends from the RAG post-cleavage complex (PCC) to the non-homologous end joining (NHEJ) machinery to promote appropriate antigen receptor gene assembly. However, this transfer mechanism is poorly understood, partly because of the technical difficulty in revealing weak association of coding ends (CEs) with one of the PCCs, coding end complex (CEC). Using fluorescence resonance energy transfer (FRET) and anisotropy measurement, we present here real-time monitoring of the RAG1/2-catalyzed cleavage reaction, and provide unequivocal evidence that CEs are retained within the CEC in the presence of Mg 2+ . By examining the dynamic fluorescence changes during the cleavage reaction, we compared the stability of CEC assembled with core RAG1 paired with full-length RAG2, core RAG2 or a frameshift RAG2 mutant that was speculated to destabilize the PCC, leading to increased aberrant joining. While the latter two CECs exhibit similar stability, the full-length RAG2 renders a less stable CEC unless H3K4me3 peptides are added. Interestingly, the RAG2 mutant appears to modulate the structure of the RAG-12RSS pre-cleavage complex. Thus, the fluorescence-based detection offers a sensitive, quantitative and continuous assessment of pre-cleavage complex assembly and CEC stability.
    Keywords: Recombination
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2014-05-01
    Description: The teicoplanin-associated locus regulator (TcaR) regulates gene expression of proteins on the intercellular adhesion (ica) locus involved in staphylococci poly- N -acetylglucosamine biosynthesis. The absence of TcaR increases poly- N -acetylglucosamine production and promotes biofilm formation. Until recently, the mechanism of multiple antibiotic resistance regulator family protein members, such as TcaR, was restricted to binding double-stranded DNA. However, we recently found that TcaR strongly interacts with single-stranded DNA, which is a new role for this family of proteins. In this study, we report Staphylococcus epidermidis TcaR–single-stranded DNA complex structures. Our model suggests that TcaR and single-stranded DNA form a 6 1 -symmetry polymer composed of TcaR dimers with single-stranded DNA that wraps outside the polymer and 12 nt per TcaR dimer. Single-stranded DNA binding to TcaR involves a large conformational change at the DNA binding lobe. Several point mutations involving the single-stranded DNA binding surface validate interactions between single-stranded DNA and TcaR. Our results extend the novel role of multiple antibiotic resistance regulator family proteins in staphylococci.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2013-12-11
    Description: [1]  Cyclones are responsible for much of the high impact weather in the extratropics, thus how they will change under global warming is of great concern. Several studies have used the multi-model climate simulations conducted under Phase 5 of the Coupled Model Intercomparison Project (CMIP5) to examine such changes. One study suggested that the frequency of strong cyclones is projected to decrease over the North Pacific, while another concluded that this frequency will increase. [2]  A single tracking algorithm has been used to derive cyclone statistics from 23 CMIP5 simulations using two different definitions of cyclones: cyclones as minima in total sea level pressure (SLP), or cyclones as minima in SLP perturbations about a large scale, low frequency background. When cyclones are defined by total SLP, the frequency of deep cyclones over the Pacific is projected to increase, while if cyclones are defined as perturbations, this frequency is projected to decrease. These differences are shown to be due to a projected deepening of the climatological mean Aleutian low. [3]  In view of these results, it is important to critically assess how cyclones should be defined. Preliminary results suggest that among CMIP5 simulations, over the Pacific, both the projected changes in the frequency of high wind events and mean available potential energy are better correlated with the projected changes in the frequency of cyclones defined as perturbations. It is concluded that more research should be done to quantify and understand the impacts of the different definitions of cyclones.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
    Publication Date: 2014-08-27
    Description: : MSstats is an R package for statistical relative quantification of proteins and peptides in mass spectrometry-based proteomics. Version 2.0 of MSstats supports label-free and label-based experimental workflows and data-dependent, targeted and data-independent spectral acquisition. It takes as input identified and quantified spectral peaks, and outputs a list of differentially abundant peptides or proteins, or summaries of peptide or protein relative abundance. MSstats relies on a flexible family of linear mixed models. Availability and implementation: The code, the documentation and example datasets are available open-source at www.msstats.org under the Artistic-2.0 license. The package can be downloaded from www.msstats.org or from Bioconductor www.bioconductor.org and used in an R command line workflow. The package can also be accessed as an external tool in Skyline ( Broudy et al. , 2014 ) and used via graphical user interface. Contact: ovitek@purdue.edu
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 6
    Publication Date: 2012-12-15
    Description: CMIP5 multimodel ensemble projection of midlatitude storm track changes has been examined. Storm track activity is quantified by temporal variance of meridional wind and sea level pressure (psl), as well as cyclone track statistics. For the Southern Hemisphere (SH), CMIP5 models project clear poleward migration, upward expansion, and intensification of the storm track. For the Northern Hemisphere (NH), the models also project some poleward shift and upward expansion of the storm track in the upper troposphere/lower stratosphere, but mainly weakening of the storm track toward its equatorward flank in the troposphere. Consistent with these, CMIP5 models project significant increase in the frequency of extreme cyclones during the SH cool season, but significant decrease in such events in the NH. Comparisons with CMIP3 projections indicate high degrees of consistency for SH projections, but significant differences are found in the NH. Overall, CMIP5 models project larger decrease in storm track activity in the NH troposphere, especially over North America in winter, where psl variance as well as cyclone frequency and amplitude are all projected to decrease significantly. In terms of climatology, similar to CMIP3, most CMIP5 models simulate storm tracks that are too weak and display equatorward biases in their latitude. These biases have also been related to future projections. In the NH, the strength of a model's climatological storm track is negatively correlated with its projected amplitude change under global warming, while in the SH, models with large equatorward biases in storm track latitude tend to project larger poleward shifts.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
    Publication Date: 2013-01-20
    Description: The mRNA export complex TREX (TREX) is known to contain Aly, UAP56, Tex1 and the THO complex, among which UAP56 is required for TREX assembly. Here, we systematically investigated the role of each human TREX component in TREX assembly and its association with the mRNA. We found that Tex1 is essentially a subunit of the THO complex. Aly, THO and UAP56 are all required for assembly of TREX, in which Aly directly interacts with THO subunits Thoc2 and Thoc5. Both Aly and THO function in linking UAP56 to the cap-binding protein CBP80. Interestingly, association of UAP56 with the spliced mRNA, but not with the pre-mRNA, requires Aly and THO. Unexpectedly, we found that Aly and THO require each other to associate with the spliced mRNA. Consistent with these biochemical results, similar to Aly and UAP56, THO plays critical roles in mRNA export. Together, we propose that Aly, THO and UAP56 form a highly integrated unit to associate with the spliced mRNA and function in mRNA export.
    Keywords: Computational Methods, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 8
    Publication Date: 2013-12-29
    Description: MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database ( http://mirtarbase.mbc.nctu.edu.tw/ ) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for 〉100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2014-07-13
    Description: A 12-m diameter radio telescope will be deployed to the Summit Station in Greenland to provide direct confirmation of a Super Massive Black Hole (SMBH) by observing its shadow image in the active galaxy M87. The telescope (Greenland Telescope: GLT) is to become one of the Very Long Baseline Interferometry (VLBI) stations at sub-millimeter (submm) regime, providing the longest baseline 〉 9,000 km to achieve an exceptional angular resolution of 20 µas at 350 GHz, which will enable us to resolve the shadow size of ~40 µas. The triangle with the longest baselines formed by the GLT, the Atacama Large Millimeter/submillimeter Array (ALMA) in Chile, and the Submillimeter Array (SMA) in Hawaii will play a key role for the M87 observations. We have been working on the image simulations based on realistic conditions for a better understanding of the possible observed images. In parallel, retrofitting of the telescope and the site developments are in progress. Based on three years of opacity monitoring at 225 GHz, our measurements indicate that the site is excellent for submm observations, comparable to the ALMA site. The GLT is also expected to make single-dish observations up to 1.5 THz.
    Print ISSN: 0048-6604
    Electronic ISSN: 1944-799X
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
    Publication Date: 2013-04-09
    Description: [1]  Many studies have attempted to estimate the equilibrium climate sensitivity (CS) to the doubling of CO 2 concentrations. One common methodology is to compare versions of Earth Models of Intermediate Complexity (EMICs) to spatially and/or temporally averaged historical observations. Despite the persistent efforts, CS remains uncertain. It is, thus far, unclear what is driving this uncertainty. Moreover, the effects of the internal climate variability on the CS estimates obtained using this method have not received thorough attention in the literature. [2]  Using a statistical approximator (“emulator”) of an EMIC, we show in an observation system simulation study, that unresolved internal climate variability appears to be a key driver of CS uncertainty (as measured by the 68% credible interval). We first simulate many realizations of pseudo-observations from an emulator at a “true” prescribed CS, and then re-estimate the CS using the pseudo-observations and an inverse parameter estimation method. [3]  We demonstrate that a single realization of the internal variability can result in a sizable discrepancy between the best CS estimate and the truth. Specifically, the average discrepancy is 0.84 °C, with the feasible range up to several °C. The results open the possibility that recent climate sensitivity estimates from global observations and EMICs are systematically considerably lower or higher than the truth, since they are typically based on the same realization of climate variability. This possibility should be investigated in future work. We also find that estimation uncertainties increase at higher climate sensitivities, suggesting that a high CS might be difficult to detect.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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