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Open Access Publications from the University of California

Scholarly Works (32 results)

  • Article
Mester, Volume 37 (2008)
[No abstract]
    Cover page: Una charla con Diamela Eltit
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2014)
    Patients harboring brain arteriovenous malformation (bAVM) are at life-threatening risk of rupture and intracranial hemorrhage (ICH). The pathogenesis of bAVM has not been completely understood. Current treatment options are invasive, and ≈ 20 % of patients are not offered interventional therapy because of excessive treatment risk. There are no specific medical therapies to treat bAVMs. The lack of validated animal models has been an obstacle for testing hypotheses of bAVM pathogenesis and testing new therapies. In this review, we summarize bAVM model development and bAVM pathogenesis and potential therapeutic targets that have been identified during model development.
      Cover page: Brain Arteriovenous Malformation Modeling, Pathogenesis, and Novel Therapeutic Targets
      • Article
      • Peer Reviewed
      The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

      Enhancing the zinc (Zn) in wheat (Triticum aestivum L.) grain is a breeding aim in order to improve human Zn nutrition. This study analyses the temporal dynamics of Zn concentrations in grain tissues during grain filling. On examination of Zn distribution in grains of plants grown at either 1 or 5 mg Zn kg-1 soil, the Zn concentration of the crease was found to increase by 5 to 9 fold between 7 and 34 DAA, while that of the endosperm decreased by 7 to 45%. Because the Zn turnover rate (d-1) in the crease tissues was either independent of the Zn application level or higher at the lower Zn application level, and the Zn concentration increased with time during grain filling while the turnover rate gradually decreased, it seems that the process of transfer within the grain beyond the grain crease limits the endosperm allocation rather than the input of Zn into the grain. Our data do not allow us to establish whether sink strength for Zn in the endosperm or the Zn transport capacity of the involved membranes is limiting.

        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2013)
        Bacterial strains CNX-216(T) and CNU-914(T) were isolated from marine sediment samples collected from Palmyra Atoll and off Catalina Island, respectively. Both strains were gram-negative and aerobic and produce deep-orange to pink colonies and alkaloid secondary metabolites. Cells of strain CNX-216(T) were short, non-motile rods, whereas cells of strain CNU-914(T) were short, curved rods with gliding motility. The DNA G+C contents of CNX-216(T) and CNU-914(T) were respectively 57.7 and 44.4 mol%. Strains CNX-216(T) and CNU-914(T) contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1ω5c as the major fatty acids. Phylogenetic analyses revealed that both strains belong to the order Cytophagales in the phylum Bacteroidetes. Strain CNX-216(T) exhibited low 16S rRNA gene sequence identity (87.1 %) to the nearest type strain, Cesiribacter roseus 311(T), and formed a well-supported lineage that is outside all currently described families in the order Cytophagales. Strain CNU-914(T) shared 97.6 % 16S rRNA gene sequence identity with 'Porifericola rhodea' N5EA6-3A2B and, together with 'Tunicatimonas pelagia' N5DB8-4 and four uncharacterized marine bacteria isolated as part of this study, formed a lineage that is clearly distinguished from other families in the order Cytophagales. Based on our polyphasic taxonomic characterization, we propose that strains CNX-216(T) and CNU-914(T) represent novel genera and species, for which we propose the names Mooreia alkaloidigena gen. nov., sp. nov. (type strain CNX-216(T)  = DSM 25187(T)  = KCCM 90102(T)) and Catalinimonas alkaloidigena gen. nov., sp. nov. (type strain CNU-914(T)  = DSM 25186(T)  = KCCM 90101(T)) within the new families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov.
          Cover page: Mooreia alkaloidigena gen. nov., sp. nov. and Catalinimonas alkaloidigena gen. nov., sp. nov., alkaloid-producing marine bacteria in the proposed families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. in the phylum Bacteroidetes.
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2011)
          Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%-50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3' untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation.
            Cover page: Complex and dynamic landscape of RNA polyadenylation revealed by PAS-SeqCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Irvine Previously Published Works (2008)
            We demonstrate the use of optical coherence tomography (OCT) as a non-destructive diagnostic tool for evaluating laser-processing performance by imaging the features of a pit and a rim. A pit formed on a material at different laser-processing conditions is imaged using both a conventional scanning electron microscope (SEM) and OCT. Then using corresponding images, the geometrical characteristics of the pit are analyzed and compared. From the results, we could verify the feasibility and the potential of the application of OCT to the monitoring of the laser-processing performance.
              Cover page: Three-dimensional non-destructive optical evaluation of laser-processing performance using optical coherence tomographyCreative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UC Irvine Previously Published Works (2010)
              We report a photonic crystal fiber (PCF) coupler having an ultrawide spectral bandwidth keeping single mode operation. The use of the PCF coupler in a fiber-based optical coherence tomography (OCT) system enables us to handle the wide spectral bands of various light sources, including superluminescent diodes (SLDs) at 1300 nm and 820 nm, Ti:sapphire lasers, and white-light sources. The multiband imaging performances of the PCF-based OCT system are demonstrated by obtaining dental images at 1300 nm and 820 nm with the same setup. In addition, we show that the PCF coupler could cover the spectrum over a one octave span and guide both the fundamental wave (1030 nm) and the second harmonic wave (515 nm) simultaneously.
                Cover page: Ultrawideband photonic crystal fiber coupler for multiband optical imaging system.Creative Commons 'BY' version 4.0 license
                • Article
                • Peer Reviewed
                The Proceedings of the International Plant Nutrition Colloquium XVI (2009)

                Boron (B) is an essential trace element for higher plants yet it becomes toxic when present at high concentrations. The site of B toxicity in plant roots is located in the root tip, and B tolerance is associated with the concentration of reducing sugars (RS) in this region. In the study reported here, we aimed to detect and map loci associated with this trait using a barley doubled-haploid population derived from a cross between Clipper (B sensitive) and Sahara 3771 (B tolerant). The population was screened at high B supply using solution culture, with the RS concentration measured in the root tip. The RS concentration varied widely in the parents and DH lines, ranging from 14 to 141 mg g-1. Using a linkage map of 420 molecular markers, quantitative trait loci (QTL) were detected on chromosomes 2H, 3H, 5H and 6H. Of these, the QTL on 2H had the largest effect, explaining 16% of the phenotypic variance, with the (high RS) allele contributed from Sahara 3771. QTLs detected here were co-located with reported loci for other B tolerance traits, including leaf symptom, relative root elongation and B uptake, indicating a role of RS in physiological pathways associated with B tolerance.

                  Cover page: Quantitative trait loci for reducing sugar concentration in the barley root tip under boron toxicity
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                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2013)

                  Background and purpose

                  Bone marrow-derived cells (BMDCs) home to vascular endothelial growth factor (VEGF)-induced brain angiogenic foci, and VEGF induces cerebrovascular dysplasia in adult endoglin heterozygous (Eng(+/-)) mice. We hypothesized that Eng(+/-) BMDCs cause cerebrovascular dysplasia in the adult mouse after VEGF stimulation.

                  Methods

                  BM transplantation was performed using adult wild-type (WT) and Eng(+/-) mice as donors/recipients. An adeno-associated viral vector expressing VEGF was injected into the basal ganglia 4 weeks after transplantation. Vascular density, dysplasia index (vessels >15 µm/100 vessels), and BMDCs in the angiogenic foci were analyzed.

                  Results

                  The dysplasia index of WT/Eng(+/-) BM mice was higher than WT/WT BM mice (P<0.001) and was similar to Eng(+/-)/Eng(+/-) BM mice (P=0.2). Dysplasia in Eng(+/-) mice was partially rescued by WT BM (P<0.001). WT/WT BM and WT/Eng(+/-) BM mice had similar numbers of BMDCs in the angiogenic foci (P=0.4), most of which were CD68(+). Eng(+/-) monocytes/macrophages expressed less matrix metalloproteinase-9 and Notch1.

                  Conclusions

                  Endoglin-deficient BMDCs are sufficient for VEGF to induce vascular dysplasia in the adult mouse brain. Our data support a previously unrecognized role of BM in the development of cerebrovascular malformations.
                    Cover page: Endoglin Deficiency in Bone Marrow is Sufficient to Cause Cerebrovascular Dysplasia in the Adult Mouse After Vascular Endothelial Growth Factor Stimulation
                    • Article
                    • Peer Reviewed
                    UC San Diego Previously Published Works (2015)
                    Low-nutrient media and long incubation times facilitated the cultivation of 20 taxonomically diverse Gram-negative marine bacteria within the phyla Bacteroidetes and Proteobacteria. These strains comprise as many as three new families and include members of clades that had only been observed using culture-independent techniques. Chemical studies of the type strains representing two new families within the order Cytophagales led to the isolation of nine new alkaloid secondary metabolites that can be grouped into four distinct structure classes, including azepinones, aziridines, quinolones, and pyrazinones. Several of these compounds possess antibacterial properties and appear, on structural grounds, to be produced by amino acid-based biosynthetic pathways. Our results demonstrate that relatively simple cultivation techniques can lead to the isolation of new bacterial taxa that are capable of the production of alkaloid secondary metabolites with antibacterial activities. These findings support continued investment in cultivation techniques as a method for natural product discovery.
                      Cover page: Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production
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