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Rationale: Human rhinovirus infections cause colds and trigger exacerbations of lower airway diseases.Objectives: To define changes in gene expression profiles during in vivo rhinovirus infections.Methods: Nasal epithelial scrapings were obtained before and during experimental rhinovirus infection, and gene expression was evaluated by microarray. Naturally acquired rhinovirus infections, cultured human epithelial cells, and short interfering RNA knockdown were used to further evaluate the role of viperin in rhinovirus infections.Measurements and Main Results: Symptom scores and viral titers were measured in subjects inoculated with rhinovirus or sham control, and changes in gene expression were assessed 8 and 48 hours after inoculation. Real-time reverse transcription-polymerase chain reaction for viperin and rhinoviruses was used in naturally acquired infections, and viperin mRNA levels and viral titers were measured in cultured cells. Rhinovirus-induced changes in gene expression were not observed 8 hours after viral infection, but 11,887 gene transcripts were significantly altered in scrapings obtained 2 days postinoculation. Major groups of up-regulated genes included chemokines, signaling molecules, interferon-responsive genes, and antivirals. Viperin expression was further examined and also was increased in naturally acquired rhinovirus infections, as well as in cultured human epithelial cells infected with intact, but not replication-deficient, rhinovirus. Knockdown of viperin with short interfering RNA increased rhinovirus replication in infected epithelial cells.Conclusions: Rhinovirus infection significantly alters the expression of many genes associated with the immune response, including chemokines and antivirals. The data obtained provide insights into the host response to rhinovirus infection and identify potential novel targets for further evaluation. [ABSTRACT FROM AUTHOR]

Background: To our knowledge, changes in the patterns of whole-transcriptome gene expression that occur during the induction and resolution of experimental gingivitis in humans were not previously explored using bioinformatic tools., Methods: Gingival biopsy samples collected from 14 subjects during a 28-day stent-induced experimental gingivitis model, followed by treatment, and resolution at days 28 through 35 were analyzed using gene-expression arrays. Biopsy samples were collected at different sites within each subject at baseline (day 0), at the peak of gingivitis (day 28), and at resolution (day 35) and processed using whole-transcriptome gene-expression arrays. Gene-expression data were analyzed to identify biologic themes and pathways associated with changes in gene-expression profiles that occur during the induction and resolution of experimental gingivitis using bioinformatic tools., Results: During disease induction and resolution, the dominant expression pathway was the immune response, with 131 immune response genes significantly up- or downregulated during induction, during resolution, or during both at P <0.05. During induction, there was significant transient increase in the expression of inflammatory and oxidative stress mediators, including interleukin (IL)-1 alpha (IL1A), IL-1 beta (IL1B), IL8, RANTES, colony stimulating factor 3 (CSF3), and superoxide dismutase 2 (SOD2), and a decreased expression of IP10, interferon inducible T-cell alpha chemoattractant (ITAC), matrix metalloproteinase 10 (MMP10), and beta 4 defensin (DEFB4). These genes reversed expression patterns upon resolution in parallel with the reversal of gingival inflammation., Conclusions: A relatively small subset (11.9%) of the immune response genes analyzed by array was transiently activated in response to biofilm overgrowth, suggesting a degree of specificity in the transcriptome-expression response. The fact that this same subset demonstrates a reversal in expression patterns during clinical resolution implicates these genes as being critical for maintaining tissue homeostasis at the biofilm-gingival interface. In addition to the immune response pathway as the dominant response theme, new candidate genes and pathways were identified as being selectively modulated in experimental gingivitis, including neural processes, epithelial defenses, angiogenesis, and wound healing.

MEDLINE is one of the most important bibliographical information sources for biologists and medical workers. Its PubMed interface supports Boolean queries, which are potentially expressive and exact. However, PubMed is also designed to support simplicity of use at the expense of query expressiveness and exactness. Many PubMed users have never tried explicit Boolean queries. We developed a Java program, PubMed Assistant, to make literature access easier in several ways. PubMed Assistant provides an interface that efficiently displays information about the citations and includes useful functions such as keyword highlighting, export to citation managers, clickable links to Google Scholar and others that are lacking in PubMed.

The core histone complex (H3:H4:H2A:H2B)2 and products of dissociation, the H2A:H2B: dimer and the H3:H4 tetramer, were isolated from chicken erythrocyte chromatin by several literature methods as well as gel filtration on Bio-Gel A15m at various salt concentrations. The conformational and oligomeric characteristic of these histone complexes were compared to analogous histone complexes prepared by renaturation of individually acid-extracted histones by circular dichroism (CD) and analytical gel filtration chromatography. The salt-extracted core histone complex (independent of method of preparation), the purified dissociation products, the H2A:H2B dimer, and the H3:H4 tetramer in 2 M NaCl, 10 mM sodium phosphate, 0.25 mM EDTA and 0.1 mM DTT, pH 7.0, have conformation which are identical, by the criteria of similar CD spectra, with complexes prepared from acid-extracted histones, Likewise, the salt-extracted complexes may be cycled through solvents of low ionic strength (10 mM sodium phosphate, pH 7.0 or 50 mM NaOAc, pH 5.0) or 1 mM HCl and returned to 2.0 M NaCl, 10 mM sodium phosphate, 0.25 mM EDTA, and 0.1 mM DTT, pH 7.0, in a completely reversible manner. Thus it would appear that acid-denatured histones are capable of being fully renatured to yield native-like complexes.

The ability of high molecular weight chicken erythrocyte chromatin to spontaneously self-assemble into native-like material, after dissociation by high ionic strength and reassociation by salt gradient dialysis, was critically examined. The native conformational state of the reassembled nucleoprotein complex was regenerated to the extent reflected by circular dichroism spectra and thermally induced helix--coil transition of the nucleoprotein DNA. However, internucleosomal packing of approximately 205 base pairs of DNA per repeating unit, as probed by digestion with micrococcal nuclease, was not regenerated upon reassembly and was replaced by a packing of approximately 160 base pairs per repeating unit. Thus, high molecular weight chromatin containing only lysine-rich histones (H1 and H5) and core histones (H2A, H2B, H3, and H4) is not a true self-assembling system in vitro using the salt gradient dialysis system used herein. Circular dichroism and thermal denaturation studies on core chromatin (lysine-rich histones removed) showed that core histones alone are not capable of reassembling high molecular weight DNA into native-like core particles at low temperature (4 degree C). Reassembly at 21 degree C restored the circular dichroism but not the thermal denaturation properties to those characteristic of undissociated core chromatin. Nonetheless, micrococcal nuclease digestions of both reassembled core chromatin products were identical with undissociated native core chromatin. Ressembly in the presence of the complete complement of histones, followed by removal of the lysine-rich histones, did regenerate the thermal denaturation properties of undissociated native core particles. These results indicated multiple functions of the lysine-rich histones in the in vitro assembly of high molecular weight chromatin.

Inactive chromatin of the chicken erythrocyte nucleus is shown to consist of two distinct classes (I and S). I chromatin (approximately 60% of the total genome) is insoluble at greater than 0.1 M ionic strength whereas S chromatin (approximately 40% of the total genome) is soluble at all ionic strengths studied (0.01--0.3 M). These chromatins are released from nuclei upon digestion with micrococcal nuclease by two separate parallel processes that do not have a precursor--product relationship to each other. Isolated I-chromatin fragments show a progressive reduction in size from 250 to approximately 50 nucleosome equivalents with increasing digestion times at 0-2 degrees C. Prolonged digestion of nuclei at 37 degrees C results in conversion of I chromatin to mononucleosomes that are insoluble at greater than 30 mM NaCl. Isolated S-chromatin fragments show a constant size distribution, independent of digestion time, that peaks at approximately 35 nucleosome equivalents. Prolonged digestion of nuclei at 37 degrees C results in the conversion of S chromatin to mononucleosomes that are soluble at physiological ionic strength. Both I and S chromatins contain a full complement of histones with no nonhistone proteins.

Sodium dodecyl sulfate (SDS) has been used to induce a dry scaly skin condition in human subjects. Measurements of stratum (s.) corneum hydration, scaliness, and lipid composition reveal in vivo surfactant perturbations on desquamation. Subjects (n = 10) were briefly treated daily with a 4% aqueous solution of SDS on one lower leg over a period of 2 weeks. The other control leg received no treatments. At the end of the treatment period, both lower legs were evaluated for hydration using an electrical impedance technique and examined by an independent dermatologist using a visually based grading scale for surface roughness and scaliness. Shave biopsies were then excised from each lower leg for analysis of s. corneum lipids. Treatment resulted in decreased s. corneum hydration and increased surface scale/roughness. These physical changes were accompanied by significant changes in s. corneum lipid composition. While surfactant treatments did not alter the total quantity of lipids per gram s. corneum protein, significant changes in specific lipid classes were observed. The free cholesterol to cholesterol ester ratio increased while the quantity of total sterols remained constant. The distribution of certain ceramide species were altered while the quantity of total ceramides remained constant. Free fatty acids were resolved into 2 distinct bands, only one of which diminished upon treatment. These results are interpreted in terms of a model for surfactant-induced perturbation of keratinization which leads to abnormal s. corneum lipids and altered desquamation.

Bulk chromatin fragments were excised from chicken erythrocyte nuclei by digestion with micrococcal nuclease. Fractionation into S chromatin (soluble at physiological ionic strengths) and I chromatin (insoluble at physiological ionic strengths) was achieved by dialysis against buffers containing 0.15 M NaCl. The effects of NaCl concentration on the molecular dimensions of S and I chromatins were determined by dynamic and static light scattering. Series of fragment lengths were obtained by gel filtration of S and I chromatins under ionic conditions which lead to maximal intramolecular compaction. Hydrodynamic radii and radii of gyration were determined for fragment lengths ranging from 8 to 53 nucleosomes. These data are in excellent agreement with calculations for extended helical structures. Close-packed solenoidal or superbead structures are not compatible with these data. Comparisons of molecular dimensions derived from light scattering and electron microscopy indicate that considerable shrinkage of chromatin fragments can occur when common methods of sample preparation are used for microscopy.

Low molecular weight histone complexes of H2A (congruent to dimer), H2B (congruent to tetramer), H3--H4 (congruent to tetramer), H2A--H2B (congruent to dimer), and H2B--H4 (congruent to dimer) have been prepared in 2 M NaCl and neutral pH at 4 degrees C. These materials are free of nonspecific aggregate and are suitable for study by high resolution proton magnetic resonance spectroscopy. Such spectra have been recorded in aqueous solutions under conditions allowing a study of the exchangeable proton resonances of histone complexes for the first time and indicate that the structured regions are rich in hydrophobic amino acids, as well as arginine and some acidic amino acids. Most of the lysine and probably alanine residues remain in a motile, random coil-like state after formation of the complexes. It is suggested that arginine residues may be important in inter- and/or intra-subunit interactions in histone complexes.

The glycine-arginine-rich histone, f2al (IV) (102 amino acids), from calf thymus was cleaved at residue 84 with cyanogen bromide. Complexes containing homologous DNA and each f2al fragment were reconstituted by means of Gdn-HC1 gradient dialysis. The circular dichroic (CD) spectra of these complexes were all examined in 0.14 M NaC1. The CD spectra of the DNA-f2al fragment complexes did not differ appreciably from that of DNA alone in the wavelength region above 240 nm. However, intact f2al-DNA complexes yield CD spectra which differ significantly (enhanced, blue-shifted, 273-nm band) from that of native DNA (Shih and Fasman, 1971). The small C-terminal fragment (85-102) was bound weakly to DNA under the conditions used. However, the large basic N-terminal fragment (1-83) was bound as well to DNA as was whole f2al, but produced no CD distortion. The conformation of the N-terminal fragment, unlike intact f2al, was not changed upon increasing the ionic strength to 0.14 M NaF. These results complement previous studies on f2al and its N-terminal CNBr fragment (Ziccardi and Schumaker, 1973). Thermal denaturation of the complexes in 2.5 X 10(-4) M EDTA was monitored simultaneously by changes in the absorption and CD spectra. All complexes showed a thermal transition at 45 degrees (Tml), attributable to the melting of free, double-stranded DNA. In addition, f2al-DNA and N fragment-DNA complexes displayed melting phenomena at 88 and 78 degrees (Tm2), respectively, caused by the denaturation of the histone-bound DNA. This difference in Tm2 constitutes further evidence that loss of the 18-amino-acid carboxyl end segment of f2al prohibits the unique type of interaction which occurs between DNA and the intact histone.