Unique contribution of IRF-5-Ikaros axis to the B-cell IgG2a response.

IRF-5 is a transcription factor activated by toll like receptor (TLR)7 and TLR9 during innate immune responses. IRF-5 activates not only Type I IFN, but also inflammatory cytokines. Most importantly, a genetic variation in the IRF-5 gene shows a strong association with autoimmune diseases such as Lupus. Here, we report that IRF5-deficient mice have attenuated IgG2a/c responses to T-cell-dependent and -independent antigens and to polyoma virus infection. This defect is due to the intrinsic deletion of IRF-5 in B cells, as SCID mice reconstituted with Irf5-/- B cells show a decrease in IgG2a/c expression after viral infection compared with mice that received wild-type B cells. Irf5-/-B cells in vitro have diminished TLR and cytokine-induced class switching to IgG2a/c. Addressing the molecular mechanism, we show that IRF-5 regulates IgG2a/c expression by decreasing Ikaros expression; reconstitution of IRF-5 in Irf5-/- B cells downregulates Ikaros levels and increases switching to IgG2a/c. The IRF site in ikzf1 promoter binds IRF-5, IRF-4 and IRF-8. We show that IRF-8 but not IRF-4 activates the ikzf1 promoter, and IRF-5 inhibits the transcriptional activity of IRF-8. Collectively, these results identify the IRF-5-Ikaros axis as a critical modulator of IgG2a/c class switching.

In vitro glucuronidation of the antibacterial triclocarban and its oxidative metabolites.

Triclocarban (3,4,4'-trichlorocarbanilide; TCC) is widely used as an antibacterial in bar soaps. During use of these soaps, a significant portion of TCC is absorbed by humans. For the elimination from the body, glucuronidation plays a key role in both biliary and renal clearance. To investigate this metabolic pathway, we performed microsomal incubations of TCC and its hydroxylated metabolites 2'-OH-TCC, 3'-OH-TCC, and 6-OH-TCC. Using a new liquid chromatography-UV-mass spectrometry method, we could show a rapid glucuronidation for all OH-TCCs by the uridine-5'-diphosphate-glucuronosyltransferases (UGT) present in liver microsomes of humans (HLM), cynomolgus monkeys (CLM), rats (RLM), and mice (MLM). Among the tested human UGT isoforms, UGT1A7, UGT1A8, and UGT1A9 showed the highest activity for the conjugation of hydroxylated TCC metabolites followed by UGT1A1, UGT1A3, and UGT1A10. Due to this broad pattern of active UGTs, OH-TCCs can be efficiently glucuronidated in various tissues, as shown for microsomes from human kidney (HKM) and intestine (HIM). The major renal metabolites in humans, TCC-N-glucuronide and TCC-N'-glucuronide, were formed at very low conversion rates (<1%) by microsomal incubations. Low amounts of N-glucuronides were generated by HLM, HIM, and HKM, as well as by MLM and CLM, but not by RLM, according to the observed species specificity of this metabolic pathway. Among the human UGT isoforms, only UGT1A9 had activity for the N-glucuronidation of TCC. These results present an anomaly where in vivo the predominant urinary metabolites of TCC are N and N'-glucuronides, but these compounds are slowly produced in vitro.

Independently switchable atomic quantum transistors by reversible contact reconstruction.

The controlled fabrication of actively switchable atomic-scale devices, in particular transistors, has remained elusive to date. Here, we explain the operation of an atomic-scale three-terminal device by a novel switching mechanism of bistable, self-stabilizing reconstruction of the electrode contacts at the atomic level: While the device is manufactured by electrochemical deposition, it operates entirely on the basis of mechanical effects of the solid-liquid interface. We analyze mechanically and thermally stable metallic junctions with a predefined quantized conductance of 1-5 G0 in experiment and atomistic simulation. Atomistic modeling of structural and conductance properties elucidates bistable electrode reconstruction as the underlying mechanism of the device. Independent room temperature operation of two transistors at low voltage demonstrates intriguing perspectives for quantum electronics and logics on the atomic scale.

Electronic excitations of glycine, alanine, and cysteine conformers from first-principles calculations.

The electronic and optical properties are studied for three conformers of amino acid molecules using gradient-corrected (spin-) density functional theory within a projector-augmented wave scheme and the supercell method. We investigate single-particle excitations such as ionization energies and electron affinities as well as pair excitations. By comparing eigenvalues resulting from several local and nonlocal energy functionals, the influence of treatment of exchange and correlation is demonstrated. The excitations are described within the Delta-self-consistent field method with an occupation number constraint to obtain excitation energies and Stokes shifts. The results are used to also discuss the optical absorption properties. In contrast to the lowest single- and two-particle excitation energies, remarkable changes are found in absorption spectra in dependence on the conformation of the molecule geometry.

DFT studies using supercells and projector-augmented waves for structure, energetics, and dynamics of glycine, alanine, and cysteine.

A large variety of gas phase conformations of the amino acids glycine, alanine, and cysteine is studied by numerically efficient semi-local gradient-corrected density functional theory calculations using a projector-augmented wave scheme and periodic boundary conditions. Equilibrium geometries, conformational energies, dipole moments, vibrational modes, and IR optical spectra are calculated from first principles. A comparison of our results with values obtained from quantum-chemistry methods with localized basis sets and nonlocal exchange-correlation functionals as well as with experimental data is made. For conformations containing strong intramolecular hydrogen bonds deviations in their energetic ordering occur, which are traced back to different treatments of spatial nonlocality in the exchange-correlation functional. However, even for these structures, the comparison of calculated and measured vibrational frequencies shows satisfying agreement.

Characterization of mouse epithelial protein lost in neoplasm (EPLIN) and comparison of mammalian and zebrafish EPLIN.

EPLIN is a cytoskeleton-associated protein that was initially identified as the product of a gene that is transcriptionally down-regulated in cancer cells. In human, there are two known isoforms, EPLIN-alpha and -beta, generated by alternative promoter usage from a single gene. With the exception of a single LIM (lin-11, isl-1, and mec-3) domain, the sequence of EPLIN is unique and does not provide any clues to its function. To identify conserved regions of EPLIN that may be important for its function, we have characterized mouse (m) and zebrafish (zf) EPLIN. As in human, two isoforms, the 593 aa mEPLIN-alpha (77% identity; 83% similarity) and 753 aa mEPLIN-beta (75% identity; 83% similarity), were present in mouse. mEPLIN-alpha is highly expressed in embryonic tissue and adult lung and spleen, whereas mEPLIN-beta is preferentially expressed in kidney, testis, lung and liver. The analysis of mEPLIN gene revealed that the overall organization of the exons in mouse and human are conserved. In zebrafish, there was only one form, the 629 aa zfEPLIN, corresponding to the mammalian EPLIN-beta. Like its mammalian counterparts, ectopically expressed zfEPLIN is co-localized to the actin cytoskeleton. While the overall homology between mammalian and zebrafish EPLIN was not striking (37% identity; 50% similarity), there were seven highly conserved regions, which should be useful in structure-function studies of this novel protein.

Characterization of the human EPLIN (Epithelial Protein Lost in Neoplasm) gene reveals distinct promoters for the two EPLIN isoforms.

EPLIN is a novel LIM domain protein that co-localizes to the actin stress fibers and focal adhesion plaques. We previously have demonstrated that two isoforms, the 600aa EPLIN-alpha and the 759aa EPLIN-beta, are generated from a single gene. In the majority of human breast and prostate cancer cell lines, the expression of EPLIN-alpha is significantly reduced, while the expression of EPLIN-beta is either up-regulated or unchanged. To understand the basis of this differential regulation, we have determined the organization of the human EPLIN gene. The human EPLIN100kb and consists of 11 exons. The EPLIN-beta mRNA requires all 11 exons, while the EPLIN-alpha mRNA requires Exons 4-11. The transcriptional start sites of EPLIN-alpha were mapped within the third intron by 5' RACE and S1 nuclease protection. Similarly, the 5' ends of EPLIN-beta were mapped upstream of Exon 1. The DNA sequences flanking the EPLIN-alpha or EPLIN-beta transcriptional start sites were capable of stimulating the expression of promoter reporter constructs. Interestingly, the endogenous transcription of EPLIN-alpha, but not EPLIN-beta, could be stimulated by serum, indicating that the expression of two EPLIN isoforms can be independently regulated. A consensus serum response element was present within 100bp upstream of the transcriptional start sites of EPLIN-alpha. The activity of 0.7kb EPLIN-alpha promoter reporter construct could be enhanced by activated RhoA, indicating that this serum response element is functional.

EPLIN, epithelial protein lost in neoplasm.

We have identified a novel cytoskeletal protein, EPLIN (Epithelial Protein Lost In Neoplasm), that is preferentially expressed in human epithelial cells. Two EPLIN isoforms, a 600 amino acid EPLIN-alpha and a 759 amino acid EPLIN-beta, are detected in primary epithelial cells of oral mucosa, prostate and mammary glands. The expression of EPLIN-alpha is either down-regulated or lost in the majority of oral cancer cell lines (8/8), prostate cancer cell lines (4/4) and xenograft tumors (3/3), and breast cancer cell lines (5/6). The amino acid sequence of EPLIN is characterized by the presence of a single centrally located LIM domain. Both EPLIN isoforms localize to filamentous actin and suppress cell proliferation when overexpressed. These findings indicate that the loss of EPLIN seen in cancer cells may play a role in cancer progression.

Identification of a cell type-specific enhancer in the distal 5'-region of the platelet-derived growth factor A-chain gene.

Transient transfection analysis of DNA subfragments from the distal 5'-flanking region of the human platelet-derived growth factor A-chain gene (-18.3 to -1.8 kilobase pairs (kb)) revealed enhancer and silencer elements that contribute significantly to transcriptional regulation. Two adjacent regions (-8.2 to -7.5 kb and -7.5 to -7.0 kb) enhanced transcription of both A-chain and heterologous thymidine kinase promoters, whereas repression was observed in two other nearby regions (-9.9 to -8.2 kb and -7.0 to -5. 9 kb). The -7.5 to -7.0-kb fragment, or J, was the strongest enhancer, and its activity was localized to a 66-base pair element (A-chain cell type-specific enhancer (ACE 66)). ACE66 activity was highly cell type-specific, with greatest activity seen in choriocarcinoma cell lines (4-10-fold enhancement). Progressive 5'- and 3'-deletions of the ACE66 revealed distribution of activity across the element, with nucleotides 1-33 being critical for function. Electrophoretic mobility shift assays revealed cell type-specific patterns of high affinity protein binding to the element. Ethylation interference footprinting of JEG-3 extract localized guanine contacts on nucleotides 1-18 of both strands of the ACE element, whereas more extensive contacts were made with the phosphate backbone (nucleotides 1-32). The ACE66 element is a potent transcriptional regulator in placental cells and represents a valuable model of long distance regulation in a growth factor gene.

Repression of platelet-derived growth factor A-chain gene transcription by an upstream silencer element. Participation by sequence-specific single-stranded DNA-binding proteins.

Platelet-derived growth factor A-chain is a potent mitogen expressed in a restricted number of normal and transformed cells. Transient transfection and deletion analysis in BSC-1 (African green monkey, renal epithelial) cells revealed that the -1680 to -1374 region of the A-chain gene repressed homologous and heterologous promoter activities by 60-80%. An S1 nuclease-hypersensitive region (5'SHS) was identified within this region (-1418 to -1388) that exhibited transcriptional silencer activity in BSC-1 and a variety of human tumor cell lines (U87, HepG2, and HeLa). Electrophoretic mobility shift assays conducted with 5'SHS oligodeoxynucleotide probes revealed several binding protein complexes that displayed unique preferences for binding to sense, antisense, and double-stranded forms of the element. Southwestern blot analysis revealed that the antisense strand of 5'SHS binds to nuclear proteins of molecular mass 97, 87, 44, and 17 kDa, whereas the double-stranded form of 5'SHS is recognized by a 70-kDa factor. Mutations within 5'SHS element indicated the necessity of a central 5'-GGGGAGGGGG-3' motif for protein binding and silencer function, while nucleotides flanking both sides of the motif were also critical for repression. These results support a model in which silencer function of 5'SHS is mediated by antisense strand binding proteins, possibly by stabilizing single-stranded DNA conformations required for interaction with enhancer sequences in the proximal promoter region of the A-chain gene.

Platelet-derived growth factor A-chain gene transcription is mediated by positive and negative regulatory regions in the promoter.

Platelet-derived growth factor (PDGF) is a disulphide-linked heterodimer of two polypeptide chains, the A and B chains, which are encoded by genes on separate chromosomes. The A-chain gene is transcribed in a number of transformed and non-transformed cell lines and is inducible by a wide variety of growth factors, cytokines and other mitogenic agonists. To localize DNA elements that mediate basal transcription in the promoter regulatory region of the A-chain gene, we have employed 5'-endpoint deletion mutagenesis and transient expression analysis in the renal epithelial cell line BSC-1 (African green monkey). Studies conducted in this cell line, which expresses high concentrations of PDGF A-chain mRNA, reveal a positive regulatory element (PRE) in a GC-rich stretch of the A-chain promoter between -82 and -40, relative to the transcription start site. Two discrete regions of the promoter were identified as negative regulatory elements (NREs), located between -1029 and -880 (NRE1) and between -1800 and -1029 (NRE2). The -1800 to -812 region, which contains both NREs, functions as a potent NRE when relocated in either orientation adjacent to the herpes simplex virus thymidine kinase promoter, reducing transcription activity by 60% in the positive orientation and 85% in the negative orientation. Comparison of BSC-1 cells and Saos-2 cells (human osteogenic sarcoma), which do not express significant quantities of PDGF A-chain mRNA or protein, indicates that basal transcription of the gene is determined by enhancer activity mediated by the GC-rich region rather than through de-repression of the upstream NREs. Electrophoretic gel mobility shift assays reveal a complex pattern of nuclear protein binding to the GC-rich PRE (-73 to -46). Competition studies conducted with mutant oligonucleotides that alternately disrupt consensus binding sites for Sp-1 or Egr-1 demonstrate a requirement for the presence of an Sp1-like core sequence (GGCGGG) but not Egr-1/Krox-24 [GCG(G/T)-GGGCG] for the formation of specific DNA-protein complexes. Our observations suggest that basal transcription of the A-chain gene in renal epithelial cells is achieved through active enhancement, mediated by a GC-rich PRE and nuclear proteins that bind to Sp-1-like consensus DNA sequences.

Colonic-crypt-derived epithelia express induced ion transport differentiation in monolayer cultures on permeable matrix substrata.

The processes of transport differentiation from stem cell to the terminally differentiated cell in intact colonic crypts are difficult to study because access to the lumen is limited. Colonocytes were isolated from the lower two-thirds of rat distal colon crypts and grown to confluence on reconstituted basement membranes and permeable support in primary culture. Crypt and surface cells were distinguished by the uptake of [3H]thymidine and [3H]leucine and by brushborder fluorescence binding. Ion concentrations in apical and basolateral compartments of filter monolayer cultures after 48 h of incubation on days 16-18 were (in mM): apical, Na+ 116 +/- 4 (n = 48) and K+ 6 +/- 1 (n = 48); basolateral, Na+ 151 +/- 3 and K+ 3.7 +/- 0.5, respectively (mean +/- SE). Aldosterone (10(-8) M), added to the basolateral compartment from days 10-18, changed apical Na+ to 72 +/- 6 mM and apical K+ to 13 +/- 4 mM (n = 23). Dexamethasone (10(-8) M) changed apical Na+ to 84 +/- 7 mM but did not influence apical K+ (n = 22). Transmonolayer electrical potential difference (VtM; control medium; days 8-10) was 5 +/- 1 mV (n = 16; apical compartment negative); electrical resistance (RtM) was 217 +/- 21 omega.cm2 and short circuit current (ISC) was 21 +/- 5 microA.cm-2. Amiloride (0.1 mM; n = 12) in the apical medium decreased VtM to 2 +/- 1 mV and ISC to 11 +/- 4 microA.cm-2. Aldosterone (10(-8) M) after 1 week in the basolateral compartment (n = 21) changed VtM to 12.3 +/- 3 mV, RtM to 92 +/- 9 omega.cm2, and ISC to 138 +/- 23 microA.cm-2. Apical amiloride (0.1 mM; n = 9) decreased the induced VtM to -3 +/- 1 mV and ISC to -13 +/- 7 microA.cm-2. Colonic-crypt-derived epithelial cells proliferate and differentiate in primary culture, when grown on reconstituted basement membrane substratum and in supplemented medium, to form monolayers that express net Na+ absorption and net K+ secretion after 1 week. Na+ and K+ vectorial transport differentiation is primarily regulated by aldosterone, which specifically induces apical conductive Na+ transfer. Mineralocorticoid and glucocorticoid hormones appear to have differing actions on ion transport in functionally surface-type colonocytes derived in culture from isolated crypt-type cells.