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Open Access Publications from the University of California

Scholarly Works (18 results)

  • Article
  • Peer Reviewed
UC Riverside Previously Published Works (2005)

The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign orthologs based on the similarity between DNA or protein sequences may make erroneous assignments when sequence similarity does not clearly delineate the evolutionary relationship among genes of the same families. In this paper, we present a new approach to ortholog assignment that takes into account both sequence similarity and evolutionary events at a genome level, where orthologous genes are assumed to correspond to each other in the most parsimonious evolving scenario under genome rearrangement. First, the problem is formulated as that of computing the signed reversal distance with duplicates between the two genomes of interest. Then, the problem is decomposed into two new optimization problems, called minimum common partition and maximum cycle decomposition, for which efficient heuristic algorithms are given. Following this approach, we have implemented a high-throughput system for assigning orthologs on a genome scale, called SOAR, and tested it on both simulated data and real genome sequence data. Compared to a recent ortholog assignment method based entirely on homology search (called INPARANOID), SOAR shows a marginally better performance in terms of sensitivity on the real data set because it is able to identify several correct orthologous pairs that are missed by INPARANOID. The simulation results demonstrate that SOAR, in general, performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs.

    Cover page: Assignment of orthologous genes via genome rearrangement
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2006)

    Background: Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets. Results: OLIGOSPAWN is a suite of software tools that offers two complementary services, namely (1) the selection of "unique" oligos each of which appears in one unigene but does not occur (exactly or approximately) in any other and (2) the selection of "popular" oligos each of which occurs (exactly or approximately) in as many unigenes as possible. In this paper, we describe the functionalities of OLIGOSPAWN and the computational methods it employs, and we report on experimental results for the overgo probes designed with it. Conclusion: The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of several tens of Mb in a few hours on a regular PC. The software has been used to design overgo probes employed to screen a barley BAC library (Hordeum vulgare). OLIGOSPAWN is freely available at http://oligospawn.ucr.edu/.

      Cover page: OligoSpawn: a software tool for the design of overgo probes from large unigene datasets
      • Article
      • Peer Reviewed
      California Breast Cancer Research Program Funded Publications (1996)
        Cover page: Molecular cloning and characterization of human FGF8 alternative messenger RNA forms
        • Article
        • Peer Reviewed
        UC San Francisco Previously Published Works (2012)
        The unfolded protein response (UPR) monitors the protein folding capacity of the endoplasmic reticulum (ER). In all organisms analyzed to date, the UPR drives transcriptional programs that allow cells to cope with ER stress. The non-conventional splicing o
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2014)
          In this study, we have carried out paleointensity experiments on 918 specimens spanning the last ~7 kyr, including pottery fragments, baked clay and slag, collected from Shandong, Liaoning, Zhejiang and Hebei Provinces in China. Approximately half of the specimens yielded results that passed strict data selection criteria and give high-fidelity paleointensities. The virtual axial dipole moments (VADMs) of our sites range from ~2×1022to ~13×1022Am2. At ~2250 BCE our results suggest a paleointensity low of ~2×1022Am2, which increases to a high of ~13×1022Am2by ~1300 BCE. This rapid (less than 1000 yrs) six-fold change in the paleointensity may have important implications for the dynamics of core flow at this time. Our data from the last ~3 kyr are generally in good agreement with the ARCH3k.1 model, but deviate significantly at certain time periods from the CALS3k.4 and CALS10k.1b model, which is likely due to differences in the data used to constrain these models. At ages older than ~3 ka, where only the CALS10k.1b model is available for comparison, our data deviate significantly from the model. Combining our new results with the published data from China and Japan, we provide greatly improved constraints for the regional model of Eastern Asia. When comparing the variations of geomagnetic field in three global representative areas of Eastern Asia, the Middle East and Southern Europe, a common general trend of sinusoidal variations since ~8 ka is shown, likely dominated by the dipole component. However, significant disparities are revealed as well, which we attribute to non-dipolar components caused by movement of magnetic flux patches at the core-mantle boundary. © 2014 Elsevier B.V.
            Cover page: Geomagnetic intensity variations for the past 8 kyr: New archaeointensity results from Eastern China
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2013)
            Argonaute proteins are often credited for their cytoplasmic activities in which they function as central mediators of the RNAi platform and microRNA (miRNA)-mediated processes. They also facilitate heterochromatin formation and establishment of repressive
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2014)
              Black carbon (BC) was characterized by three complementary techniques - incandescence (single particle soot photometer, SP2, at Parque Morelos), light absorption (cavity ringdown spectrometer with integrating nephelometer, CRDS-Neph, at Parque Morelos and Aethalometers at seven locations), and volatility (volatility tandem differential mobility analyzer, V-TDMA) during the Cal-Mex 2010 campaign. SP2, CRDS-Neph, and Aethalometer measurements characterized the BC mass, and SP2 and V-TDMA measurements also quantified BC-containing particle number, from which mass-mean BC diameters were calculated. Onaverage, the mass concentrations measured in Tijuana (1.8±2.6μgm-3 at Parque Morelos and 2.6μgm-3 in other regions of Tijuana) were higher than in San Diego or the international border crossing (0.5±0.6μgm-3). The observed BC mass concentrations were attributable to nighttime urban burning activities and diesel vehicles, both from the local (Baja California) and transported (Southern California) diesel vehicle fleets. Comparisons of the SP2 and co-located Aethalometers indicated that the two methods measured similar variations in BC mass concentrations (correlation coefficients greater than 0.85), and the mass concentrations were similar for the BC particles identified from nighttime urban burning sources. When the BC source changed to diesel vehicle emissions, the SP2 mass concentrations were lower than the Aethalometer mass concentrations by about 50%, likely indicating a change in the mass absorption efficiency and quantification by the Aethalometers. At Parque Morelos there were up to three different-sized modes of BC mass in particles: one mode below 100nm, one near 100nm, and another between 200 and 300nm. The mode between 200 and 300nm was associated with urban burning activities that influenced the site during evening hours. When backtrajectories indicated that airmasses came from the south to the Parque Morelos site, BC mass in particles was also larger (mass median diameter of 170nm rather than 155nm), consistent with the higher fraction of older diesel vehicles in the Tijuana fleet compared to the vehicles found in southern California. © 2013 Elsevier Ltd.
                Creative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2013)
                Quantification of minimal residual disease (MRD) following allogeneic hematopoietic cell transplantation (allo-HCT) predicts post-transplant relapse in patients with chronic lymphocytic leukemia (CLL). We utilized an MRD-quantification method that amplifie
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2020)
                  Delayed graft function due to transplant ischemia/reperfusion injury adversely affects up to 50% of deceased-donor kidney transplant recipients. However, key factors contributing to the severity of ischemia/reperfusion injury remain unclear. Here, using a clinically relevant mouse model of delayed graft function, we demonstrated that donor genetic background and kidney-intrinsic MyD88/Trif-dependent innate immunity were key determinants of delayed graft function. Functional deterioration of kidney grafts directly corresponded with the duration of cold ischemia time. The graft dysfunction became irreversible after cold ischemia time exceeded six hours. When cold ischemia time reached four hours, kidney grafts displayed histological features reflective of delayed graft function seen in clinical kidney transplantation. Notably, kidneys of B6 mice exhibited significantly more severe histological and functional impairment than kidneys of C3H or BALB/c mice, regardless of recipient strains or alloreactivities. Furthermore, allografts of B6 mice also showed an upregulation of IL-6, neutrophil gelatinase-associated lipocalin, and endoplasmic reticulum stress genes, as well as an increased influx of host neutrophils and memory CD8 T-cells. In contrast, donor MyD88/Trif deficiency inhibited neutrophil influx and decreased the expression of IL-6 and endoplasmic reticulum stress genes, along with improved graft function and prolonged allograft survival. Thus, kidney-intrinsic factors involving genetic characteristics and innate immunity serve as critical determinants of the severity of delayed graft function. This preclinical murine model allows for further investigations of the mechanisms underlying delayed graft function.
                    Cover page: Kidney-intrinsic factors determine the severity of ischemia/reperfusion injury in a mouse model of delayed graft function
                    • Article
                    • Peer Reviewed
                    UC Irvine Previously Published Works (2009)
                    Measurements of hydroxyl ( OH) and hydroperoxy (HO2) radicals were made during the Mexico City Metropolitan Area (MCMA) field campaign as part of the MILAGRO (Megacity Initiative: Local and Global Research Observations) project during March 2006. These measurements provide a unique opportunity to test current models of atmospheric ROx (OH + HO2 + RO2) photochemistry under polluted conditions. A zero-dimensional box model based on the Regional Atmospheric Chemical Mechanism (RACM) was constrained by 10-min averages of 24 J-values and the concentrations of 97 chemical species. Several issues related to the ROx chemistry under polluted conditions are highlighted in this study: (i) Measured concentrations of both OH and HO2 were underpredicted during morning hours on a median campaign basis, suggesting a significant source of radicals is missing from current atmospheric models under polluted conditions, consistent with previous urban field campaigns. (ii) The model-predicted HO2/OH ratios underestimate the measurements for NO mixing ratios higher than 5 ppb, also consistent with previous urban field campaigns. This suggests that under high NOx conditions, the HO2 to OH propagation rate may be overestimated by the model or a process converting OH into HO2 may be missing from the chemical mechanism. On a daily basis ( 08: 40 a. m.-06: 40 p. m.), an analysis of the radical budget indicates that HONO photolysis, HCHO photolysis, O-3-alkene reactions and dicarbonyls photolysis are the main radical sources. O-3 photolysis contributes to less than 6% of the total radical production.
                    • 1 supplemental PDF
                    Cover page: Measurements of OH and HO<sub>2</sub> concentrations during the MCMA-2006 field campaign - Part 2: Model comparison and radical budgetCreative Commons 'BY' version 4.0 license
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