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Le C, Stuckey DC. Impact of feed carbohydrates and nitrogen source on the production of soluble microbial products (SMPs) in anaerobic digestion. WATER RESEARCH 2017; 122:10-16. [PMID: 28587911 DOI: 10.1016/j.watres.2017.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/12/2017] [Accepted: 05/28/2017] [Indexed: 06/07/2023]
Abstract
Six stirred fill-and-draw batch reactors with a range of carbohydrate feeds (glucose, fructose and sucrose), and nitrogen sources (NH4Cl, urea) at various concentrations were used to investigate the effect of feed composition on the production of soluble microbial products (SMPs) during anaerobic digestion (AD). To gain greater insights into the SMPs produced, the composition of various fractions was analyzed, while the low molecular weight (MW) SMPs generated with different feeds and nutrients were collected and chemically analyzed using GC-MS. Other organic solutes such as free amino acids were determined using HPLC, and this level of chemical analysis has never been carried out in past work because of analytical limitations. It was found that the presence of ammonium salts rather than urea at 200 mg/L stimulated the production of not only volatile fatty acids, but also SMPs of different MW fractions, and reduced the production of biogas significantly. The study also revealed that the type of SMP that dominates in a particular system depends on the chemical characteristics of the feed, and this insight has implications on the composition of the effluent from anaerobic digesters (and their potential chlorination by-products), and membrane fouling in membrane bioreactors.
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Affiliation(s)
- Chencheng Le
- Advanced Environmental Biotechnology Center, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore; Division of Environmental and Water Resources Engineering, School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
| | - David C Stuckey
- Advanced Environmental Biotechnology Center, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore; Department of Chemical Engineering, Imperial College London, SW7 2AZ, UK.
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2
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Diversification of the primary antibody repertoire begins during early follicle development in the rabbit appendix. Mol Immunol 2012; 54:140-7. [PMID: 23270685 DOI: 10.1016/j.molimm.2012.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 11/12/2012] [Accepted: 11/12/2012] [Indexed: 11/20/2022]
Abstract
Rabbits generate a diversified primary antibody repertoire by somatically mutating, in gut-associated lymphoid tissue (GALT), an initial repertoire that is limited by preferential rearrangement of the 3'-most IGVH gene segment. To determine when repertoire diversification begins in GALT, we performed in situ hybridization on neonatal rabbit appendix sections with an activation-induced cytidine deaminase (AID) riboprobe, because AID is required for the mutational processes that diversify the primary antibody repertoire. We first detected AID mRNA expression around 1 week of age, in the basal region of developing follicles. By PCR-amplifying V-D-J genes from AID mRNA(+) B cells isolated by laser capture microdissection, we found evidence of somatic hypermutation, and one likely instance of somatic gene conversion. Our results suggest that V-(D)-J gene diversification begins during early postnatal appendix development, in B cells stimulated to enter a proliferative program by signals derived from select intestinal commensals.
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Activation-induced cytidine deaminase alters the subcellular localization of Tet family proteins. PLoS One 2012; 7:e45031. [PMID: 23028748 PMCID: PMC3444495 DOI: 10.1371/journal.pone.0045031] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 08/11/2012] [Indexed: 01/09/2023] Open
Abstract
Activation-induced cytidine deminase (Aid), a unique enzyme that deaminates cytosine in DNA, shuttles between the nucleus and the cytoplasm. A recent study proposed a novel function of Aid in active DNA demethylation via deamination of 5-hydroxymethylcytosine, which is converted from 5-methylcytosine by the Ten-eleven translocation (Tet) family of enzymes. In this study, we examined the effect of simultaneous expression of Aid and Tet family proteins on the subcellular localization of each protein. We found that overexpressed Aid is mainly localized in the cytoplasm, whereas Tet1 and Tet2 are localized in the nucleus, and Tet3 is localized in both the cytoplasm and the nucleus. However, nuclear Tet proteins were gradually translocated to the cytoplasm when co-expressed with Aid. We also show that Aid-mediated translocation of Tet proteins is associated with Aid shuttling. Here we propose a possible role for Aid as a regulator of the subcellular localization of Tet family proteins.
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Honjo T, Kobayashi M, Begum N, Kotani A, Sabouri S, Nagaoka H. The AID dilemma: infection, or cancer? Adv Cancer Res 2012; 113:1-44. [PMID: 22429851 DOI: 10.1016/b978-0-12-394280-7.00001-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Activation-induced cytidine deaminase (AID), which is both essential and sufficient for forming antibody memory, is also linked to tumorigenesis. AID is found in many B lymphomas, in myeloid leukemia, and in pathogen-induced tumors such as adult T cell leukemia. Although there is no solid evidence that AID causes human tumors, AID-transgenic and AID-deficient mouse models indicate that AID is both sufficient and required for tumorigenesis. Recently, AID's ability to cleave DNA has been shown to depend on topoisomerase 1 (Top1) and a histone H3K4 epigenetic mark. When the level of Top1 protein is decreased by AID activation, it induces irreversible cleavage in highly transcribed targets. This finding and others led to the idea that there is an evolutionary link between meiotic recombination and class switch recombination, which share H3K4 trimethyl, topoisomerase, the MRN complex, mismatch repair family proteins, and exonuclease 3. As Top1 has recently been shown to be involved in many transcription-associated genome instabilities, it is likely that AID took advantage of basic genome instability or diversification to evolve its mechanism for immune diversity. AID targets are therefore not highly specific to immunoglobulin genes and are relatively abundant, although they have strict requirements for transcription-induced H3K4 trimethyl modification and repetitive sequences prone to forming non-B structures. Inevitably, AID-dependent cleavage takes place in nonimmunoglobulin targets and eventually causes tumors. However, battles against infection are waged in the context of acute emergencies, while tumorigenesis is rather a chronic, long-term process. In the interest of survival, vertebrates must have evolved AID to prevent infection despite its long-term risk of causing tumorigenesis.
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Hori N, Iwasa F, Tsukimura N, Sugita Y, Ueno T, Kojima N, Ogawa T. Effects of UV photofunctionalization on the nanotopography enhanced initial bioactivity of titanium. Acta Biomater 2011; 7:3679-91. [PMID: 21723964 DOI: 10.1016/j.actbio.2011.06.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 05/13/2011] [Accepted: 06/14/2011] [Indexed: 10/18/2022]
Abstract
This study addresses the control of the biological capabilities of titanium through specific nanosurface features and its potential modulation by UV photofunctionalization. Rat bone marrow derived osteoblasts were cultured on titanium disks with micropits alone, micropits with 100 nm nodules, micropits with 300 nm nodules, or micropits with 500 nm nodules, with or without UV treatment. After a 24 h incubation protein adsorption, as well as the attachment, retention, and spread of osteoblasts were examined in correlation with the topographical parameters of the titanium substrates. Each of the biological events was governed by a different set of multiple surface topographical factors with a distinctive pattern of regulation. For instance, without UV treatment the protein adsorption and cell attachment capability of titanium substrates increased linearly with increasing average roughness (Ra) and surface area of titanium disks, but increased polynomially with increasing nanonodule diameter. The cell retention capability increased polynomially with increasing nanonodular diameter and Ra, but increased linearly with increasing surface area. Consequently, the micropits with 300 nm nodules created the most favorable environment for this initial osteoblast behavior and response. UV treatment of the nanonodular titanium surfaces resulted in considerable enhancement of all biological events. However, the pattern of UV-mediated enhancement was disproportionate; exponential and overriding effects were observed depending upon the biological event and topographical parameter. As an example of overriding enhancement, the cell retention capability, which fluctuated with changes in various topographical parameters, became invariably high after UV treatment. The present data provide a basis for understanding how to optimize nanostructures to create titanium surfaces with increased biological capabilities and uncover a novel advantage of UV photofunctionalization of titanium substrates that synergistically increases its nanotopography enhanced biological capabilities whereby most of the initial biological events of osteoblasts were overwhelmingly enhanced beyond a simple proportional increase.
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Rai G, Ray S, Milton J, Yang J, Ren P, Lempicki R, Mage RG. Gene expression profiles in a rabbit model of systemic lupus erythematosus autoantibody production. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2010; 185:4446-56. [PMID: 20817871 PMCID: PMC2949067 DOI: 10.4049/jimmunol.1001254] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We previously reported the establishment of a rabbit (Oryctolagus cuniculus) model in which peptide immunization led to production of lupus-like autoantibodies including anti-Sm, -RNP, -SS-A, -SS-B, and -dsDNA characteristic of those produced in systemic lupus erythematosus (SLE) patients. Some neurologic symptoms in the form of seizures and nystagmus were observed. The animals used in the previous and in the current study were from a National Institute of Allergy and Infectious Diseases colony of rabbits that were pedigreed, Ig-allotype defined, but not inbred. Their genetic heterogeneity may correspond to that found among patients of a given ethnicity. We extended the information about this rabbit model by microarray-based expression profiling. We first demonstrated that human expression arrays could be used with rabbit RNA to yield information on molecular pathways. We then designed a study evaluating gene expression profiles in eight groups of control and treated rabbits (47 rabbits in total). Genes significantly upregulated in treated rabbits were associated with NK cytotoxicity, Ag presentation, leukocyte migration, cytokine activity, protein kinases, RNA spliceosomal ribonucleoproteins, intracellular signaling cascades, and glutamate receptor activity. These results link increased immune activation with upregulation of components associated with neurologic and anti-RNP responses, demonstrating the utility of the rabbit model to uncover biological pathways related to SLE-induced clinical symptoms, including neuropsychiatric lupus. Our finding of distinct gene expression patterns in rabbits that made anti-dsDNA compared with those that only made other anti-nuclear Abs should be further investigated in subsets of SLE patients with different autoantibody profiles.
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Affiliation(s)
- Geeta Rai
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892
| | - Satyajit Ray
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892
| | - Jacqueline Milton
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892
| | - Jun Yang
- Laboratory of Bioinformatics and Immunopathogenesis, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD, 21702, USA
| | - Ping Ren
- Laboratory of Bioinformatics and Immunopathogenesis, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD, 21702, USA
| | - Richard Lempicki
- Laboratory of Bioinformatics and Immunopathogenesis, SAIC-Frederick, Inc., NCI-Frederick, Frederick, MD, 21702, USA
| | - Rose G. Mage
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-1892
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7
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Electrostatic control of protein adsorption on UV-photofunctionalized titanium. Acta Biomater 2010; 6:4175-80. [PMID: 20466081 DOI: 10.1016/j.actbio.2010.05.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 04/22/2010] [Accepted: 05/06/2010] [Indexed: 11/23/2022]
Abstract
Ultraviolet (UV)-photofunctionalization of titanium to enable the establishment of a nearly complete bone-implant contact was reported recently. However, the underlying mechanism for this is unknown. We hypothesized that UV-treated titanium surfaces acquire distinct electrostatic properties that may play important roles in determining the bioactivity of these surfaces. The objective of this study was to determine the protein adsorption capability of UV-treated titanium surfaces under various electrostatic environments. The amount of albumin adsorbed on UV-treated and untreated titanium disks was evaluated under different pH conditions above and below the isoelectric points of albumin and titanium. The effects of additional treatment with various ionic solutions were also examined. Albumin adsorption on UV-treated surfaces at pH 7.0 was considerably greater (6-fold after 3h of incubation and 2.5-fold after 24h) than that to UV-untreated surfaces. UV-enhanced albumin adsorption was abrogated at pH 3.0 or when these titanium surfaces were treated with anions, while maintaining UV-induced superhydrophilicity. Albumin adsorption on UV-untreated titanium surfaces increased after treating these surfaces with divalent cations but not after treating them with monovalent cations. These results indicated that UV-treated titanium surfaces are electropositively charged as opposed to electronegatively charged UV-untreated titanium surfaces. This distinct UV-induced electrostatic property predominantly regulates the protein adsorption capability of titanium, superseding the effect of hydrophilic status, and converts titanium surfaces from bioinert to bioactive. As a result, direct titanium-protein interactions take place exclusively on UV-treated titanium surfaces without the aid of bridging ions.
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8
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Borchert GM, Holton NW, Edwards KA, Vogel LA, Larson ED. Histone H2A and H2B are monoubiquitinated at AID-targeted loci. PLoS One 2010; 5:e11641. [PMID: 20661291 PMCID: PMC2905439 DOI: 10.1371/journal.pone.0011641] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 06/18/2010] [Indexed: 11/24/2022] Open
Abstract
Background Somatic hypermutation introduces base substitutions into the rearranged and expressed immunoglobulin (Ig) variable regions to promote immunity. This pathway requires and is initiated by the Activation Induced Deaminase (AID) protein, which deaminates cytidine to produce uracils and UG mismatches at the Ig genes. Subsequent processing of uracil by mismatch repair and base excision repair factors contributes to mutagenesis. While selective for certain genomic targets, the chromatin modifications which distinguish hypermutating from non-hypermutating loci are not defined. Methodology/Principal Findings Here, we show that AID-targeted loci in mammalian B cells contain ubiquitinated chromatin. Chromatin immunoprecipitation (ChIP) analysis of a constitutively hypermutating Burkitt's B cell line, Ramos, revealed the presence of monoubiquitinated forms of both histone H2A and H2B at two AID-associated loci, but not at control loci which are expressed but not hypermutated. Similar analysis using LPS activated primary murine splenocytes showed enrichment of the expressed VH and Sγ3 switch regions upon ChIP with antibody specific to AID and to monoubiquitinated H2A and H2B. In the mechanism of mammalian hypermutation, AID may interact with ubiquitinated chromatin because confocal immunofluorescence microscopy visualized AID colocalized with monoubiquitinated H2B within discrete nuclear foci. Conclusions/Significance Our results indicate that monoubiquitinated histones accompany active somatic hypermutation, revealing part of the histone code marking AID-targeted loci. This expands the current view of the chromatin state during hypermutation by identifying a specific nucleosome architecture associated with somatic hypermutation.
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Affiliation(s)
- Glen M. Borchert
- School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America
| | - Nathaniel W. Holton
- School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America
| | - Kevin A. Edwards
- School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America
| | - Laura A. Vogel
- School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America
| | - Erik D. Larson
- School of Biological Sciences, Illinois State University, Normal, Illinois, United States of America
- * E-mail:
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9
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Suzuki T, Kubo K, Hori N, Yamada M, Kojima N, Sugita Y, Maeda H, Ogawa T. Nonvolatile buffer coating of titanium to prevent its biological aging and for drug delivery. Biomaterials 2010; 31:4818-28. [PMID: 20350765 DOI: 10.1016/j.biomaterials.2010.02.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 02/23/2010] [Indexed: 11/20/2022]
Abstract
The osseointegration capability of titanium decreases over time. This phenomenon, defined as biological aging of titanium, is associated with the disappearance of hydrophilicity and the progressive accumulation of hydrocarbons on titanium surfaces. The objective of this study was to examine whether coating of titanium surfaces with 4-(2-Hydroxylethyl)-1-piperazineethanesulfonic acid (HEPES) buffer, a nonvolatile zwitterionic chemical buffering agent, could prevent the time-dependent degradation of the bioactivity of titanium. Commercially pure titanium samples, prepared as disks and cylinders, were acid-etched with H(2)SO(4). A third of the samples were used for experiments immediately after processing (new surfaces), while another third were stored under dark ambient conditions for 3 months (3-month-old surfaces). The remaining third were coated with HEPES after acid-etching and were stored for 3 months (HEPES-coated 3-month-old surfaces). The 3-month-old surfaces were hydrophobic, while new and HEPES-coated 3-month-old surfaces were superhydrophilic. Protein adsorption and the number of osteoblasts attached during an initial culture period were substantially lower for 3-month-old surfaces than for new and HEPES-coated 3-month-old surfaces. Alkaline phosphatase activity and calcium deposition in osteoblast cultures were reduced by more than 50% on 3-month-old surfaces compared to new surfaces, whereas such degradation was not found on HEPES-coated 3-month-old surfaces. The strength of in vivo bone-implant integration for 3-month-old implants, evaluated by the push-in test, was 60% lower than that for new implants. The push-in value of HEPES-coated 3-month-old implants was equivalent to that of new implants. Coating titanium surfaces with HEPES containing an antioxidant amino acid derivative, N-acetyl cysteine (NAC), further enhanced osteoblast attachment to the surfaces, along with the increase level of intracellular glutathione reserves as a result of cellular uptake of NAC. These results suggest that HEPES coating of titanium surfaces maintained their superhydrophilicity for at least 3 months and resulted in a continuous retention of bioactivity and osteoconductivity similar to freshly prepared surfaces. This coating technology may be useful for preventing biological aging of titanium and delivering biological molecules for synergistic enhancement of bone-titanium integration.
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Affiliation(s)
- Takeo Suzuki
- Laboratory for Bone and Implant Sciences (LBIS), The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, UCLA School of Dentistry, 10833 Le Conte Avenue (B3-081 CHS), Box 951668, Los Angeles, CA 90095-1668, USA
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Quantitation of cytokine mRNA by real-time RT-PCR during a vaccination trial in a rabbit model of fascioliasis. Vet Parasitol 2009; 169:82-92. [PMID: 20056331 DOI: 10.1016/j.vetpar.2009.12.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Revised: 12/11/2009] [Accepted: 12/11/2009] [Indexed: 11/23/2022]
Abstract
Use of the rabbit as disease model has long been hampered by a lack of immunological assays specific to this species. In the present study we developed a SYBR Green-based, real-time RT-PCR protocol to quantitate cytokine mRNA in freshly harvested rabbit peripheral mononuclear cells. The method was validated in the course of a vaccination trial in which animals vaccinated with the recombinant antigen FhSAP2 were challenged with Fasciola hepatica metacercariae. Changes in the levels of rabbit interleukin (IL)-2, IL-4, IL-6, IL-10, tumor necrosis factor-alpha (TNFalpha), and interferon-gamma (IFNgamma) mRNA were determined. Messenger RNA from the universally expressed housekeeping gene GAPDH was used as an amplification control and allowed for correction of variations in the efficiencies of RNA extraction and reverse transcription. Rabbits vaccinated with FhSAP2 showed an 83.3% reduction in liver fluke burden after challenge infection when compared to non-vaccinated controls. All cytokine mRNAs were found at detectable levels; however, the levels of IFNgamma, TNFalpha, IL-2 and IL-10 were significantly higher in the vaccinated group compared to the non-vaccinated group. These results suggest that protection conferred by FhSAP2 protein could be associated with a mixed Th1/Th2 immune response in which Th1 cytokines are dominant. The real-time RT-PCR method described herein can be a useful tool for monitoring changes in basic immune functions in the rabbit model of fascioliasis and may also aid in studies of human diseases for which the rabbit is an important experimental model.
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11
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Ordinario EC, Yabuki M, Larson RP, Maizels N. Temporal regulation of Ig gene diversification revealed by single-cell imaging. THE JOURNAL OF IMMUNOLOGY 2009; 183:4545-53. [PMID: 19748985 DOI: 10.4049/jimmunol.0900673] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rearranged Ig V regions undergo activation-induced cytidine deaminase (AID)-initiated diversification in sequence to produce either nontemplated or templated mutations, in the related pathways of somatic hypermutation and gene conversion. In chicken DT40 B cells, gene conversion normally predominates, producing mutations templated by adjacent pseudo-V regions, but impairment of gene conversion switches mutagenesis to a nontemplated pathway. We recently showed that the activator, E2A, functions in cis to promote diversification, and that G(1) phase of cell cycle is the critical window for E2A action. By single-cell imaging of stable AID-yellow fluorescent protein transfectants, we now demonstrate that AID-yellow fluorescent protein can stably localize to the nucleus in G(1) phase, but undergoes ubiquitin-dependent proteolysis later in cell cycle. By imaging of DT40 polymerized lactose operator-lambda(R) cells, in which polymerized lactose operator tags the rearranged lambda(R) gene, we show that both the repair polymerase Poleta and the multifunctional factor MRE11/RAD50/NBS1 localize to lambda(R), and that lambda(R)/Poleta colocalizations occur predominately in G(1) phase, when they reflect repair of AID-initiated damage. We find no evidence of induction of gamma-H2AX, the phosphorylated variant histone that is a marker of double-strand breaks, and Ig gene conversion may therefore proceed by a pathway involving templated repair at DNA nicks rather than double-strand breaks. These results lead to a model in which Ig gene conversion initiates and is completed or nearly completed in G(1) phase. AID deaminates ssDNA, and restriction of mutagenesis to G(1) phase would contribute to protecting the genome from off-target attack by AID when DNA replication occurs in S phase.
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Affiliation(s)
- Ellen C Ordinario
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195, USA
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12
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Verma S, Goldammer T, Aitken R. Cloning and expression of activation induced cytidine deaminase from Bos taurus. Vet Immunol Immunopathol 2009; 134:151-9. [PMID: 19766322 DOI: 10.1016/j.vetimm.2009.08.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 07/21/2009] [Accepted: 08/24/2009] [Indexed: 12/13/2022]
Abstract
Activation induced cytidine deaminase is an enzyme crucial to somatic hypermutation and gene conversion, processes that are essential for the diversification of Ig V genes. The bovine Ig repertoire appears to be diversified by mechanisms that are significantly different to those that operate in humans and mice. This study set out to test the hypothesis that differences in the organization, coding sequence, expression or genomic location of the bovine AICDA gene enables the encoded enzyme to catalyse the unusual Ig diversification mechanism seen in cattle as well as conventional antigen-driven mutation. Characterization of bovine AICDA excluded the first two possibilities. AICDA expression was detected in lymphoid tissues from neonatal and older cattle, but AICDA cDNA could not be detected in muscle tissue. The pattern of gene expression did not therefore differ from that in other vertebrates. The AICDA cDNA was cloned and expressed successfully in Escherichia coli generating a phenotype consistent with the mutating action of this deaminase. Using a whole genome radiation hybrid panel, bovine AICDA was mapped to a region of bovine chromosome 5 syntenic with the location of human AICDA on chromosome 12. We conclude that the unusual nature of Ig diversification in cattle is unlikely to be attributable to the structure, sequence, activity or genomic location of bovine AICDA.
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Affiliation(s)
- Subhash Verma
- Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow, UK
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13
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Patenaude AM, Orthwein A, Hu Y, Campo VA, Kavli B, Buschiazzo A, Di Noia JM. Active nuclear import and cytoplasmic retention of activation-induced deaminase. Nat Struct Mol Biol 2009; 16:517-27. [PMID: 19412186 DOI: 10.1038/nsmb.1598] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 04/02/2009] [Indexed: 11/09/2022]
Abstract
The enzyme activation-induced deaminase (AID) triggers antibody diversification in B cells by catalyzing deamination and consequently mutation of immunoglobulin genes. To minimize off-target deamination, AID is restrained by several regulatory mechanisms including nuclear exclusion, thought to be mediated exclusively by active nuclear export. Here we identify two other mechanisms involved in controlling AID subcellular localization. AID is unable to passively diffuse into the nucleus, despite its small size, and its nuclear entry requires active import mediated by a conformational nuclear localization signal. We also identify in its C terminus a determinant for AID cytoplasmic retention, which hampers diffusion to the nucleus, competes with nuclear import and is crucial for maintaining the predominantly cytoplasmic localization of AID in steady-state conditions. Blocking nuclear import alters the balance between these processes in favor of cytoplasmic retention, resulting in reduced isotype class switching.
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14
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Yang J, Pospisil R, Mage RG. Expression and localization of rabbit B-cell activating factor (BAFF) and its specific receptor BR3 in cells and tissues of the rabbit immune system. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2009; 33:697-708. [PMID: 19124039 PMCID: PMC2744865 DOI: 10.1016/j.dci.2008.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2008] [Revised: 12/01/2008] [Accepted: 12/07/2008] [Indexed: 05/27/2023]
Abstract
Rabbits are widely used for vaccine development, and investigations of human infectious and autoimmune diseases such as Systemic Lupus Erythematosus (SLE). For these applications, we cloned, sequenced and expressed rabbit B-cell Activating Factor (BAFF), and localized BAFF in cells and tissues of the rabbit immune system. The rabbit homolog of the human BAFF binding site (miniBR3 peptide) within the BAFF-specific receptor BR3 was synthesized. This 26-residue core domain binds to recombinant rabbit BAFF protein. Flow cytometric analyses using purified recombinant rabbit BAFF combined with real-time PCR findings revealed that BAFF detected on peripheral blood B-cells from normal rabbits is probably complexed to BAFF receptors rather than produced by the B-cells. BAFF was detected in developing appendix of young rabbits by immunohistochemical staining suggesting that BAFF plays a role during the period following birth when rabbit B-cell development and pre-immune antibody repertoire diversification and selection is occurring.
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Affiliation(s)
- Jiahui Yang
- Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892-1892, USA
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15
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Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL, Goodman MF, Scharff MD. The biochemistry of somatic hypermutation. Annu Rev Immunol 2008; 26:481-511. [PMID: 18304001 DOI: 10.1146/annurev.immunol.26.021607.090236] [Citation(s) in RCA: 368] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Affinity maturation of the humoral response is mediated by somatic hypermutation of the immunoglobulin (Ig) genes and selection of higher-affinity B cell clones. Activation-induced cytidine deaminase (AID) is the first of a complex series of proteins that introduce these point mutations into variable regions of the Ig genes. AID deaminates deoxycytidine residues in single-stranded DNA to deoxyuridines, which are then processed by DNA replication, base excision repair (BER), or mismatch repair (MMR). In germinal center B cells, MMR, BER, and other factors are diverted from their normal roles in preserving genomic integrity to increase diversity within the Ig locus. Both AID and these components of an emerging error-prone mutasome are regulated on many levels by complex mechanisms that are only beginning to be elucidated.
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Affiliation(s)
- Jonathan U Peled
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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Brar SS, Sacho EJ, Tessmer I, Croteau DL, Erie DA, Diaz M. Activation-induced deaminase, AID, is catalytically active as a monomer on single-stranded DNA. DNA Repair (Amst) 2007; 7:77-87. [PMID: 17889624 PMCID: PMC2693009 DOI: 10.1016/j.dnarep.2007.08.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Revised: 08/03/2007] [Accepted: 08/04/2007] [Indexed: 11/18/2022]
Abstract
Hypermutation and class switch recombination of immunoglobulin genes are antigen-activated mechanisms triggered by AID, a cytidine deaminase. AID deaminates cytidine residues in the DNA of the variable and the switch regions of the immunoglobulin locus. The resulting uracil induces error-prone DNA synthesis in the case of hypermutation or DNA breaks that activate non-homologous recombination in the case of class switch recombination. In vitro studies have demonstrated that AID deaminates single-stranded but not double-stranded substrates unless AID is in a complex with RPA and the substrate is actively undergoing transcription. However, it is not clear whether AID deaminates its substrates primarily as a monomer or as a higher order oligomer. To examine the oligomerization state of AID alone and in the presence of single-stranded DNA substrates of various structures, including loops embedded in double-stranded DNA, we used atomic force microscopy (AFM) to visualize AID protein alone or in complex with DNA. Surprisingly, AFM results indicate that most AID molecules exist as a monomer and that it binds single-stranded DNA substrates as a monomer at concentrations where efficient deamination of single-stranded DNA substrates occur. The rate of deamination, under conditions of excess and limiting protein, also imply that AID can deaminate single-stranded substrates as a monomer. These results imply that non-phosphorylated AID is catalytically active as a monomer on single-stranded DNA in vitro, including single-stranded DNA found in loops similar to those transiently formed in the immunoglobulin switch regions during transcription.
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Affiliation(s)
- Sukhdev S. Brar
- Laboratory of Molecular Genetics, D3-01, National Institute of Environmental Health, Sciences/National Institutes of Health 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Elizabeth J. Sacho
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ingrid Tessmer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Deborah L. Croteau
- Laboratory of Molecular Genetics, D3-01, National Institute of Environmental Health, Sciences/National Institutes of Health 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Dorothy A. Erie
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Applied and Material Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Corresponding authors information: Dr. Marilyn Diaz, Tel. 919-541-4740, Fax, 919-541-7593, E-mail: or Dr. Dorothy Erie, Tel. 919-962-6370, Fax, 919-962-2388, E-mail:
| | - Marilyn Diaz
- Laboratory of Molecular Genetics, D3-01, National Institute of Environmental Health, Sciences/National Institutes of Health 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
- Corresponding authors information: Dr. Marilyn Diaz, Tel. 919-541-4740, Fax, 919-541-7593, E-mail: or Dr. Dorothy Erie, Tel. 919-962-6370, Fax, 919-962-2388, E-mail:
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Abstract
Functional antibody genes are assembled by V-D-J joining and then diversified by somatic hypermutation. This hypermutation results from stepwise incorporation of single nucleotide substitutions into the V gene, underpinning much of antibody diversity and affinity maturation. Hypermutation is triggered by activation-induced deaminase (AID), an enzyme which catalyzes targeted deamination of deoxycytidine residues in DNA. The pathways used for processing the AID-generated U:G lesions determine the variety of base substitutions observed during somatic hypermutation. Thus, DNA replication across the uracil yields transition mutations at C:G pairs, whereas uracil excision by UNG uracil-DNA glycosylase creates abasic sites that can also yield transversions. Recognition of the U:G mismatch by MSH2/MSH6 triggers a mutagenic patch repair in which polymerase eta plays a major role and leads to mutations at A:T pairs. AID-triggered DNA deamination also underpins immunoglobulin variable (IgV) gene conversion, isotype class switching, and some oncogenic translocations in B cell tumors.
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Affiliation(s)
- Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, H2W 1R7 Montréal, Québec, Canada.
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Godornes C, Leader BT, Molini BJ, Centurion-Lara A, Lukehart SA. Quantitation of rabbit cytokine mRNA by real-time RT-PCR. Cytokine 2007; 38:1-7. [PMID: 17521914 PMCID: PMC2041851 DOI: 10.1016/j.cyto.2007.04.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Revised: 03/19/2007] [Accepted: 04/06/2007] [Indexed: 10/23/2022]
Abstract
Fundamental understanding of rabbit immunology and the use of the rabbit as a disease model have long been hindered by the lack of immunological assays specific to this species. In the present study, we sought to develop a method to quantitate cytokine expression in rabbit cells and tissues. We report the development of a quantitative real-time RT-PCR method for measuring the relative levels of rabbit IFN-gamma, IL-2, IL-4, IL-10 and TNF-alpha mRNA. Quantitation was accomplished by comparison to a standard curve generated using plasmid DNA containing partial sequences of the relevant cytokines. Experimental studies demonstrate applicability of this assay to quantitate cytokine mRNA levels from rabbit spleen cells following mitogen stimulation. We have further utilized this assay to also examine cytokine expression in rabbit tissues during experimental syphilis infection.
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Affiliation(s)
- Charmie Godornes
- Department of Medicine, University of Washington, Seattle WA 98195
| | | | | | - Arturo Centurion-Lara
- Department of Medicine, University of Washington, Seattle WA 98195
- Department of Pathobiology, University of Washington, Seattle WA 98195
| | - Sheila A. Lukehart
- Department of Medicine, University of Washington, Seattle WA 98195
- Department of Pathobiology, University of Washington, Seattle WA 98195
- *Corresponding author: Mailing address: Sheila A. Lukehart, PhD, Department of Medicine, Box 359779, Harborview Medical Center, 325 Ninth Ave. Seattle, WA 98104, Phone 206 341 5361, Fax 206 341 5363,
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19
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Xu Z, Pone EJ, Al-Qahtani A, Park SR, Zan H, Casali P. Regulation of aicda expression and AID activity: relevance to somatic hypermutation and class switch DNA recombination. Crit Rev Immunol 2007; 27:367-97. [PMID: 18197815 PMCID: PMC2994649 DOI: 10.1615/critrevimmunol.v27.i4.60] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Expression and activity of activation-induced cytidine deaminase (AID) encoded by the aicda gene are essential for immunoglobulin (Ig) gene somatic hypermutation (SHM) and class switch DNA recombination (CSR). SHM and CSR unfold, in general, in germinal centers and/are central to the maturation of effective antibody responses. AID expression is induced by activated B-cell CD40 signaling, which is critical for the germinal center reaction, and is further enhanced by other stimuli, including interleukin-4 (IL-4) secreted from CD4+ T cells or Toll-like receptor (TLR)-activating bacterial and/or viral molecules. Integration of different intracellular signal transduction pathways, as activated by these stimuli, leads to a dynamic aicda-regulating program, which involves both positively acting trans-factors, such as Pax5, HoxC4, E47, and Irf8, and negative modulators, such as Blimp1 and Id2, to restrict aicda expression primarily to germinal center B cells. The phosphatidylinositol 3-kinase (PI 3-K), which functions downstream of activated B-cell receptor (BCR) signaling, likely plays an important role in triggering the downregulation of aicda expression in postgerminal center B cells and throughout plasmacytoid differentiation. In B cells undergoing SHM and CSR, AID activity, and, possibly, AID targeting to the Ig locus are regulated at a posttranslational level, including AID dimerization/oligomerization, nuclear/cytoplasmic AID translocation, and phosphorylation of the AID Ser38 residue by protein kinase A (PKA). Here, we discuss the role of B-cell activation signals, transcription regulation programs, and posttranslational modifications in controlling aicda expression and AID activity, thereby delineating an integrated model of modulation of SHM and CSR in the germinal center reaction.
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Affiliation(s)
- Zhenming Xu
- Center for Immunology, School of Medicine and School of Biological Sciences, University of California, Irvine, CA 92697-4120, USA
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Leader BT, VanVoorhis WC, Lukehart SA. Expression of rabbit interleukin-4 and characterization of its biologic activity on T and B-cells. Vet Immunol Immunopathol 2006; 113:421-7. [PMID: 16879875 DOI: 10.1016/j.vetimm.2006.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 06/07/2006] [Indexed: 10/24/2022]
Abstract
The purpose of the current study was to express recombinant rabbit IL-4 (rRbIL-4) and to characterize its biological activity. The cDNA of RbIL-4 was cloned into an insect cell expression vector that allowed for constitutive expression in Sf9 cells and incorporated a 6-histidine tag on the recombinant protein for purification. The purified protein corresponded to the predicted size of rRbIL-4 and was recognized by an anti-human IL-4 antibody in immunoblotting. As shown for IL-4 from other species, a dose-dependent proliferative response was observed in T-lymphoblasts cultured with rRbIL-4. rRbIL-4 also induced increased expression of MHC class II molecules on the surface of rabbit B-cells in a dose-dependent manner. These results indicate that we have produced recombinant rabbit IL-4 that exhibits expected biological activity on rabbit B and T-cells.
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Affiliation(s)
- Brandon T Leader
- Department of Pathobiology, University of Washington, Seattle, WA 98195, USA.
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