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.

Identification of Basonuclin2, a DNA-binding zinc-finger protein expressed in germ tissues and skin keratinocytes

We used a bioinformatics approach to identify Basonuclin2, the second member of the Basonuclin zinc-finger family of transcription factors. The mouse Basonuclin2 protein consists of 1049 amino acids and contains three pairs of zinc fingers in the C-terminus that show a high level of amino acid sequence similarity with Basonuclin1. In addition, other characteristic domains of Basonuclin1, such as the serine strip and a nuclear localization signal, are also present in Basonuclin2. We used genomic and in silico database analysis to identify the human and rat homologs of basonuclin2. A search of the mouse genome showed that the basonuclin2 gene maps to chromosome 4 and consists of six exons spanning approximately 300 kb. Northern blot analysis revealed multiple transcripts of basonuclin2 in tissues of the reproductive system (ovary and testis) and also in kidney and skin. We demonstrate that, as expected from sequence conservation, recombinant Basonuclin2 can bind to a sequence in the promoter of a rRNA gene previously characterized as a Basonuclin-binding site. Full-length Basonuclin2 exclusively localizes to the nucleus, indicating that it likely plays an important role in nuclear function, probably in gene regulation. Our study establishes Basonuclin2 as a novel member of the Basonuclin family. Moreover, the structural and functional similarities with Basonuclin1 suggest that Basonuclin2 may play an analogous function in germ cells and skin keratinocytes.

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.

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.

Distribution of deoxynivalenol, zearalenone, and their respective modified analogues in milling fractions of naturally contaminated wheat grains

Mycotoxins are among the most abundant contaminants in food and feed worldwide. Therefore, in the EU maximum levels are established, e.g. for the frequently occurring Fusarium toxins deoxynivalenol (DON) and zearalenone (ZEA). Additional to DON and ZEA, modified mycotoxins are present in naturally contaminated grain products contributing significantly to the exposure of humans and animals with mycotoxins. Up to now data on the spatial distribution of many (masked) mycotoxins in the kernels of wheat are missing. The aim of the present study was to investigate the amounts of DON and ZEA as well as their most abundant derivatives DON-3-glucoside (DON-3G), 3- and 15-acetyl-DON, ZEA-14- and 16-glucoside and ZEA-14-sulphate (ZEA-14S) in mill fractions of naturally contaminated wheat batches using HPLC-MS/MS. The investigated distribution pattern in ten milling fractions is comparable among the three investigated different wheat batches. Interestingly, DON and DON-3G were found to be present to similar amounts in all fractions. In bran, the levels were only slightly higher than in the endosperm. By contrast, for ZEA and ZEA-14S a significantly higher amount of toxin is located in the fibre-rich fractions. The relative mass proportion of DON-3G comprises for only between 2.9 and 11.2% of the free DON, while the relative mass proportion of ZEA-14S is estimated to even exceed the amount of free ZEA in certain fractions. Acetylated DON derivatives and ZEA-glucosides were only detected in low amounts. The experimental results show that a significant reduction of the ZEA and ZEA-14S level in wheat flour is feasible by applying milling technology strategies. However, the almost evenly distribution of DON and DON-3G in all fractions does not allow for the technological removal of relevant toxin amounts. Furthermore, the relative share of masked forms was higher for ZEA derivatives than for the DON conjugates in the investigated wheat lots.

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.

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.

Different interface orientations of pentacene and PTCDA induce different degrees of disorder

: Organic polymers or crystals are commonly used in manufacturing of today's electronically functional devices (OLEDs, organic solar cells, etc). Understanding their morphology in general and at the interface in particular is of paramount importance. Proper knowledge of molecular orientation at interfaces is essential for predicting optoelectronic properties such as exciton diffusion length, charge carrier mobility, and molecular quadrupole moments. Two promising candidates are pentacene and 3,4:9,10-perylenetetracarboxylic dianhydride (PTCDA). Different orientations of pentacene on PTCDA have been investigated using an atomistic molecular dynamics approach. Here, we show that the degree of disorder at the interface depends largely on the crystal orientation and that more ordered interfaces generally suffer from large vacancy formation.

Small molecule inhibitors of Activation-Induced Deaminase

Activation-Induced Deaminase (AID) is a cytosine deaminase that converts cytosine into uracil in DNA, which initiates a cascade of mutagenic DNA repair to introduce point mutations and double-strand breaks. Specific targeting of AID to the immunoglobulin heavy chain locus promotes somatic hypermutation in antibody variable genes for affinity maturation, and breaks in switch regions for class switch recombination (CSR). However, mis-targeting of AID to other loci could initiate tumor development and lead to greater drug resistance among cancer cells when continually expressed. To identify a small molecule inhibitor of AID, we screened ~400,000 compounds in conjunction with the NCATS core facility at NIH. Using FRET based analysis of cytosine deamination, we identified 150 potential inhibitors of AID catalytic activity. To confirm biological function, we examined their effects on CSR in an in vitro murine B-cell activation assay using CH12 cells, wherein 30 were confirmed inhibitor candidates. We then selected the top seven molecules to proceed with further characterization in wild type primary splenocytes, and found two near-identical compounds that had inhibitory activity. From these structures, we tested commercially available analogues and identified two molecules with inhibitory efficacy in the nanomolar range. Using these approaches, we hope to identify a small molecule with great efficacy and low toxicity for use as a molecular probe to further characterize AID’s intricacies, or even as a therapeutic agent.

ATM-deficiency in the absence of T cells promotes the development of B cell lymphomas with dependence on NF-kB (TUM7P.927)

The protein product of the ataxia-telangiectasia mutated gene, ATM, is a kinase that plays a central role in maintaining genomic integrity and protecting cells from oncogenic transformation. Mutations of the human ATM gene cause ataxia-telangiectasia, an autosomal recessive disorder that is associated with increased incidence of malignancies, especially lymphoid tumors. ATM-deficient mice have been useful tools to study thymic lymphomas, which occur at high frequency in these mice, but the early onset of these tumors has prevented analysis of other types of malignancies. In this study we generated ATM- and CD3ε-deficient mice that lacked T cells. These mice do not develop thymic lymphomas, but routinely develop early onset B cell lymphomas that express surface markers characteristic of mature activated B cells. These B cell lymphomas resemble human diffuse large B cell (DLBC) lymphomas and possess complex karyotypes with genetic amplifications, deletions and unbalanced translocations. Interestingly all lymphomas (10/10) contain an amplification of a 5Mb region on chromosome 18 containing MALT1. These lymphomas also express NF-kB and are dependent on MALT1 and NF-kB signaling for in vitro survival. As such they represent a mouse model for NF-kB- dependent human DLBC lymphomas of the ABC- subtype.

Molecular analysis of age-associated B cells (ABCs) (69.7)

Age-associated B cells (ABCs) are a phenotypically and functionally distinct mature B cell subset that accumulates with age. Unlike follicular (FO) B cells, ABCs do not rely on B lymphocyte stimulator (BLyS) to survive, and are likely derived from mature B cells that exhaustively expand throughout the animal’s lifespan. Because ABCs respond to innate but not adaptive stimuli, produce cytokines, and potentiate Th17 polarization, they may alter the quality of immune responses in aged animals, thereby contributing to age-associated increases in susceptibility to infection and inflammation. In order to further investigate ABC origins, relationships to other B cell subsets, and roles in immunosenescence, we have undertaken detailed gene expression and BCR repertoire analyses. Microarray results show striking differences in gene expression patterns between ABCs and FO B cells from aged and young mice. Heavy-chain gene analysis indicates that ABCs display a diverse VH repertoire, with a mutation frequency ~6-fold higher than that observed among FO B cells, indicating previous activation and concomitant somatic hypermutation. Despite this, the ratio of CDR to FWR mutations indicates a lack of antigen-mediated selection. Taken together, our results suggest that ABCs are derived from a diverse progenitor pool and reflect prior activation; however, expansion of the ABC subset either does not include selection based on CDR specificity, or involves aberrant selection.