Clifford Wang's Publications List

A genetic reporter system to gauge cell proliferation rate.

2011-09-28T18:47:49Z

In higher eukaryotes, E2F transcription factors often drive expression of genes necessary for the cell cycle, notably the G1/S phase transition. With conventional transcriptional reporter systems, expression of a reporter gene from an E2F-responsive promoter would allow one to identify the fraction of cells making this transition. Here, we have engineered an E2F-responsive genetic reporter system ...

Ryan W S Peacock, Clifford L Wang (2011) Biotechnol Bioeng 108: 9 2003-2010

Modular construction of plasmids through ligation-free assembly of vector components with oligonucleotide linkers.

2011-09-28T18:47:49Z

We have developed a modular method of plasmid construction that can join multiple DNA components in a single reaction. A nicking enzyme is used to create 5' and 3' overhangs on PCR-generated DNA components. Without the use of ligase or restriction enzymes, components are joined using oligonucleotide linkers that recognize the overhangs. By specifying the sequences of the linkers, desired component...

Jonathan A Vroom, Clifford L Wang (2008) Biotechniques 44: 7 924-926

Expression of Aire and the early wave of apoptosis in spermatogenesis.

2011-09-28T18:46:42Z

Expression of the autoimmune regulator (Aire) protein in mice and humans is thought to be restricted to the medullary epithelial and monocyte-dendritic cells of the thymus. There it mediates expression and presentation of a large variety of proteins, including those that are peripheral organ-specific and are not expressed by other thymocytes. In this way, self-reactive T lymphocytes that would att...

Claudia E Schaller, Clifford L Wang, Gabriele Beck-Engeser, Lindsie Goss, Hamish S Scott, Mark S Anderson, Matthias Wabl (2008) J Immunol 180: 3 1338-1343

AID mutates a non-immunoglobulin transgene independent of chromosomal position.

2011-09-28T18:47:49Z

It is unknown how activation-induced cytidine deaminase (AID) targets immunoglobulin (Ig) genes during somatic hypermutation. Results to date are difficult to interpret: while some results argue that Ig genes have special sequences that mobilize AID, other work shows that non-Ig transgenes mutate. In this report, we have examined the effects of the intronic mu enhancer on the somatic hypermutation...

Jahan-Yar Parsa, Wajiha Basit, Clifford L Wang, Jennifer L Gommerman, James R Carlyle, Alberto Martin (2007) Mol Immunol 44: 4 567-575

Slow, stochastic transgene repression with properties of a timer.

2011-09-28T18:46:42Z

When gene expression varies unpredictably between genetically identical organisms, this is sometimes ascribed as stochastic. With the prevalence of retroviral vectors, stochastic repression is often observed and can complicate the interpretation of outcomes. But it may also faithfully reflect characteristics of sites in the genome.

Clifford L Wang, Desirée C Yang, Matthias Wabl (2006) Genome Biol 7: 6

Activation of an oncogenic microRNA cistron by provirus integration.

2011-09-28T18:46:42Z

Retroviruses can cause tumors when they integrate near a protooncogene or tumor suppressor gene of the host. We infected >2,500 mice with the SL3-3 murine leukemia virus; in 22 resulting tumors, we found provirus integrations nearby or within the gene that contains the mir-17-92 microRNA (miRNA) cistron. Using quantitative real-time PCR, we showed that expression of miRNA was increased in these tu...

Clifford L Wang, Bruce B Wang, Gábor Bartha, Lauri Li, Namitha Channa, Mark Klinger, Nigel Killeen, Matthias Wabl (2006) Proc Natl Acad Sci U S A 103: 49 18680-18684

Hypermutation rate normalized by chronological time.

2011-09-28T18:46:42Z

It is generally believed that in cells undergoing Ig somatic hypermutation, more cell divisions result in more mutations. This is because DNA synthesis and replication is thought to play roles in the known mechanisms-cytidine deamination and subsequent conversion to thymidine, uracil-DNA glycosylase-mediated repair, mismatch repair, and DNA synthesis by error-prone polymerases. In this study, we m...

Clifford L Wang, Matthias Wabl (2005) J Immunol 174: 9 5650-5654

Tumor model-specific proviral insertional mutagenesis of the Fos/Jdp2/Batf locus.

2011-09-28T18:51:40Z

Retroviral activation of the AP-1/ATF super family member Jdp2 was recently reported to be a common event in M-MLV-induced T cell lymphoma in p27-null C57x129 mice as compared to wild type-inoculated mice but has not been found important in other models. On the basis of retroviral tag retrieval from 1190 individual Akv- and SL3-3-induced lymphomas, we here report that insertional mutagenesis into ...

M H Rasmussen, A B Sørensen, D W Morris, J C Dutra, E K Engelhard, C L Wang, J Schmidt, F S Pedersen (2005) Virology 337: 2 353-364

Mutational activity in cell line WEHI-231.

2011-09-28T18:46:42Z

The cell line WEHI-231 expresses activation-induced cytidine deaminase (AID), the enzyme that mediates hypermutation and immunoglobulin class switch recombination in activated B cells. Although both the cDNA sequence and protein expression of AID appear normal, the frequency of mutation at the endogenous immunoglobulin locus is low. In this report, we have tested the mutational activity of the cel...

Clifford L Wang, Matthias Wabl (2005) Immunogenetics 56: 11 849-853

Directed molecular evolution by somatic hypermutation.

2011-09-28T18:46:42Z

After rearrangement of immunoglobulin gene segments, the immune system evolves the antibody repertoire by mutating the immunoglobulin variable region at a high rate. While this somatic hypermutation was thought to occur only at the variable region, recent studies suggest that hypermutation can occur at locations throughout the genome. Building upon this notion, we sought to exploit this mechanism ...

Clifford L Wang, Desirée C Yang, Matthias Wabl (2004) Protein Eng Des Sel 17: 9 659-664

DNA acrobats of the Ig class switch.

2011-09-28T18:46:42Z

Small resting B lymphocytes all start out producing IgM Abs. Upon encountering Ag, the cells become activated and make a switch from IgM to other Ig classes. This class switch serves to distribute a particular V region to different Ig C regions. Each C region mediates a specialized effector function, and so, through switching, an organism can guide its Abs to various sites. Creating the new H chai...

Clifford L Wang, Matthias Wabl (2004) J Immunol 172: 10 5815-5821

Genome-wide somatic hypermutation.

2011-09-28T18:46:42Z

DNA mutagenesis is generally considered harmful. Yet activated B cells normally mutate the Ig loci. Because this somatic hypermutation is potentially dangerous, it has been hypothesized that mutations do not occur throughout the genome but instead are actively targeted to the Ig loci. Here we challenge this longstanding and widely accepted hypothesis. We demonstrate that hypermutation requires no ...

Clifford L Wang, Ryan A Harper, Matthias Wabl (2004) Proc Natl Acad Sci U S A 101: 19 7352-7356

Precise dosage of an endogenous mutagen in the immune system.

2011-09-28T18:46:42Z

Four decades ago, it was hypothesized that lymphocytes mutate the immunoglobulin loci at a rate much greater than the spontaneous rate. Over time this Ig somatic hypermutation became the prime example of in vivo, site-directed mutagenesis. But recent studies have demonstrated that this is not necessarily the case, and that hypermutation occurs not only at the Ig locus but also at various locations...

Clifford L Wang, Matthias Wabl (2004) Cell Cycle 3: 8 983-985

A murine leukemia virus with Cre-LoxP excisible coding sequences allowing superinfection, transgene delivery, and generation of host genomic deletions.

2011-09-28T18:46:42Z

To generate a replication-competent retrovirus that could be conditionally inactivated, we flanked the viral genes of the Akv murine leukemia virus with LoxP sites. This provirus can delete its envelope gene by LoxP/Cre mediated recombination and thereby allow superinfection of Cre recombinase expressing cells.

Clifford L Wang, J Graeme Hodgson, Tiffany Malek, Finn Skou Pedersen, Matthias Wabl (2004) Retrovirology 1:

A deep-sea hydrothermal vent isolate, Pseudomonas aeruginosa CW961, requires thiosulfate for Cd tolerance and precipitation.

2011-09-28T18:45:24Z

Pseudomonas aeruginosa CW961, an isolate from the vicinity of a deep-sea hydrothermal vent, grew in the presence of 5 mM Cd(2+) and removed Cd(2+) from solution. Sulfate was sufficient for growth when Cd(2+) was not present in the culture medium; however, thiosulfate was necessary for Cd(2+) precipitation and cell survival in the presence of Cd(2+).

Clifford L Wang, Samantha C Ozuna, Douglas S Clark, Jay D Keasling (2002) Biotechnol Lett 24: 8 637-641

Aerobic sulfide production and cadmium precipitation by Escherichia coli expressing the Treponema denticola cysteine desulfhydrase gene.

2011-09-28T18:45:24Z

The cysteine desulfhydrase gene of Treponema denticola was over-expressed in Escherichia coli to produce sulfide under aerobic conditions and to precipitate metal sulfide complexes on the cell wall. When grown in a defined salts medium supplemented with cadmium and cysteine, E. coli producing cysteine desulfhydrase secreted sulfide and removed nearly all of the cadmium from solution after 48 h. A ...

C L Wang, A M Lum, S C Ozuna, D S Clark, J D Keasling (2001) Appl Microbiol Biotechnol 56: 3-4 425-430

Analysis of an engineered sulfate reduction pathway and cadmium precipitation on the cell surface.

2011-09-28T18:45:24Z

We previously have genetically engineered an aerobic sulfate reduction pathway in Escherichia coli for the generation of hydrogen sulfide and demonstrated the pathway's utility in the precipitation of cadmium. To engineer the pathway, the assimilatory sulfate reduction pathway was modified so that cysteine was overproduced. Excess cysteine was then converted by cysteine desulfhydrase to an abundan...

C L Wang, D S Clark, J D Keasling (2001) Biotechnol Bioeng 75: 3 285-291

Metabolic engineering of an aerobic sulfate reduction pathway and its application to precipitation of cadmium on the cell surface.

2011-09-28T18:45:24Z

The conversion of sulfate to an excess of free sulfide requires stringent reductive conditions. Dissimilatory sulfate reduction is used in nature by sulfate-reducing bacteria for respiration and results in the conversion of sulfate to sulfide. However, this dissimilatory sulfate reduction pathway is inhibited by oxygen and is thus limited to anaerobic environments. As an alternative, we have metab...

C L Wang, P D Maratukulam, A M Lum, D S Clark, J D Keasling (2000) Appl Environ Microbiol 66: 10 4497-4502

Cadmium removal by a new strain of Pseudomonas aeruginosa in aerobic culture.

2011-09-28T18:45:24Z

A fluorescent pseudomonad (strain CW-96-1) isolated from a deep-sea vent sample grew at 30 degrees C under aerobic conditions in an artificial seawater medium and tolerated cadmium concentrations up to 5 mM. After 140 h, strain CW-96-1 removed > 99% of the cadmium from solution. Energy dispersive microanalysis revealed that the cadmium was removed by precipitation on the cell wall; sulfide product...

C L Wang, P C Michels, S C Dawson, S Kitisakkul, J A Baross, J D Keasling, D S Clark (1997) Appl Environ Microbiol 63: 10 4075-4078