2024-03-28T21:10:49Zhttp://digital.lib.washington.edu/dspace-oai/requestoai:digital.lib.washington.edu:1773/157372016-02-14T11:37:47Zcom_1773_15658com_1773_3774col_1773_15659
00925njm 22002777a 4500
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Tsai-Yu, Lin
author
Emerman, Michael
author
2006
Background: The capsid (CA) protein of HIV-1 binds with high affinity to the host protein cyclophilin A (CypA). This binding positively affects some early stage of the viral life-cycle because prevention of binding either by drugs that occupy that active site of cyclophilin A, by mutation in
HIV-1 CA, or RNAi that knocks down intracellular CypA level diminishes viral infectivity. The closely related lentivirus, SIVcpz also binds CypA, but it was thought that this interaction was limited to the HIV-1/SIVcpz lineage because other retroviruses failed to interact with CypA in a yeast two-hybrid assay.
Results: We find that diverse lentiviruses, FIV and SIVagmTAN also bind to CypA. Mutagenesis of FIV CA showed that an amino acid that is in a homologous position to the proline at amino acid 90
of HIV-1 CA is essential for FIV interactions with CypA.
Conclusion: These results demonstrate that CypA binding to lentiviruses is more widespread than previously thought and suggest that this interaction is evolutionarily important for lentiviral
infection.
Lin T, Emerman M. Cyclophilin A interacts with diverse lentiviral capsids. Retrovirology. 2006;3(1):70.
10.1186/1742-4690-3-70
http://www.retrovirology.com/content/3/1/70
http://hdl.handle.net/1773/15737
Cyclophilin A interacts with diverse lentiviral capsids
oai:digital.lib.washington.edu:1773/157462016-02-14T11:37:57Zcom_1773_15658com_1773_3774col_1773_15659
00925njm 22002777a 4500
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Schuster, Martin
author
Greenberg, E. Peter
author
2007
Background: Quorum-sensing regulation of gene expression in Pseudomonas aeruginosa is complex. Two interconnected acyl-homoserine lactone (acyl-HSL) signal-receptor pairs, 3-oxododecanoyl-HSL-LasR and butanoyl-HSL-RhlR, regulate more than 300 genes. The induction of most of the genes is delayed during growth of P. aeruginosa in complex medium, cannot be advanced
by addition of exogenous signal, and requires additional regulatory components. Many of these late genes can be induced by addition of signals early by using specific media conditions. While several factors super-regulate the quorum receptors, others may co-regulate target promoters or may affect expression posttranscriptionally.
Results: To better understand the contributions of super-regulation and co-regulation to quorumsensing gene expression, and to better understand the general structure of the quorum sensing
network, we ectopically expressed the two receptors (in the presence of their cognate signals) and another component that affects quorum sensing, the stationary phase sigma factor RpoS, early in
growth. We determined the effect on target gene expression by microarray and real-time PCR analysis. Our results show that many target genes (e.g. lasB and hcnABC) are directly responsive to
receptor protein levels. Most genes (e.g. lasA, lecA, and phnAB), however, are not significantly affected, although at least some of these genes are directly regulated by quorum sensing. The majority of promoters advanced by RhlR appeared to be regulated directly, which allowed us to
build a RhlR consensus sequence.
Conclusion: The direct responsiveness of many quorum sensing target genes to receptor protein levels early in growth confirms the role of super-regulation in quorum sensing gene expression. The
observation that the induction of most target genes is not affected by signal or receptor protein levels indicates that either target promoters are co-regulated by other transcription factors, or that
expression is controlled posttranscriptionally. This architecture permits the integration of multiple
signaling pathways resulting in quorum responses that require a "quorum" but are otherwise highly adaptable and receptive to environmental conditions.
Schuster M, Greenberg EP. Early activation of quorum sensing in Pseudomonas aeruginosa reveals the architecture of a complex regulon. BMC Genomics. 2007;8(1):287.
10.1186/1471-2164-8-287
http://www.biomedcentral.com/1471-2164/8/287
http://hdl.handle.net/1773/15746
Early activation of quorum sensing in Pseudomonas aeruginosa reveals the architecture of a complex regulon
oai:digital.lib.washington.edu:1773/158732016-02-14T11:39:58Zcom_1773_15658com_1773_3774col_1773_15659
00925njm 22002777a 4500
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Wallace, James C.
author
Korth, Marcus J.
author
Paeper, Bryan
author
Proll, Sean C.
author
Thomas, Matthew J.
author
Magness, Charles L.
author
Iadonato, Shawn P.
author
Nelson, Charles
author
Katze, Michael G.
author
2007
Background: Until recently, few genomic reagents specific for non-human primate research have been available. To address this need, we have constructed a macaque-specific high-density oligonucleotide microarray by using highly fragmented low-pass sequence contigs from the rhesus genome project together with the detailed sequence and exon structure of the human genome. Using this method, we designed oligonucleotide probes to over 17,000 distinct rhesus/human gene orthologs and increased by four-fold the number of available genes relative to our firstgeneration expressed sequence tag (EST)-derived array.
Results: We constructed a database containing 248,000 exon sequences from 23,000 human RefSeq genes and
compared each human exon with its best matching sequence in the January 2005 version of the rhesus genome project list of 486,000 DNA contigs. Best matching rhesus exon sequences for each of the 23,000 human genes were then concatenated in the proper order and orientation to produce a rhesus "virtual transcriptome." Microarray probes were designed, one per gene, to the region closest to the 3' untranslated region (UTR) of each rhesus virtual transcript. Each probe was compared to a composite rhesus/human transcript database to test for cross-hybridization potential yielding a final probe set representing 18,296 rhesus/human gene orthologs, including
transcript variants, and over 17,000 distinct genes. We hybridized mRNA from rhesus brain and spleen to both the EST- and genome-derived microarrays. Besides four-fold greater gene coverage, the genome-derived array also showed greater mean signal intensities for genes present on both arrays. Genome-derived probes showed 99.4% identity when compared to 4,767 rhesus GenBank sequence tag site (STS) sequences indicating that early stage lowpass
versions of complex genomes are of sufficient quality to yield valuable functional genomic information when
combined with finished genome information from a closely related species.
Conclusion: The number of different genes represented on microarrays for unfinished genomes can be greatly
increased by matching known gene transcript annotations from a closely related species with sequence data from
the unfinished genome. Signal intensity on both EST- and genome-derived arrays was highly correlated with probe
distance from the 3' UTR, information often missing from ESTs yet present in early-stage genome projects.
Wallace J, Korth M, Paeper B, et al. High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations. BMC Genomics. 2007;8(1):28.
10.1186/1471-2164-8-28
http://www.biomedcentral.com/1471-2164/8/28
http://hdl.handle.net/1773/15873
High-density rhesus macaque oligonucleotide microarray design using early-stage rhesus genome sequence information and human genome annotations