Microbiome and its impact on gastrointestinal atopy.

The prevalence of allergic conditions has continuously increased in the last few decades in Westernized countries. A dysbiotic gut microbiome may play an important role in the development of allergic diseases. Genetic, environmental, and dietary factors may alter the commensal microbiota leading to inflammatory dysregulation of homeostasis. Murine and human studies have begun to elucidate the role of the microbiota in the pathogenesis of atopic diseases including asthma, atopic dermatitis, and food allergies. However, the role of the microbiome in most eosinophilic gastrointestinal diseases (EGIDs) is not yet known. This review provides an overview of what is currently known about the development of tolerance from both molecular and clinical standpoints. We also look at the gut-specific microbiome and its role in atopic conditions with the hope of applying this knowledge to the understanding, prevention, and treatment of EGIDs, particularly EoE.

Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis.

Altered microbial communities are thought to play an important role in eosinophilic oesophagitis, an allergic inflammatory condition of the oesophagus. Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. However, these data consist of non-negative, highly skewed sequence counts with a large proportion of zeros. In addition, hierarchical study designs are often performed with repeated measurements or multiple samples collected from the same subject, thus requiring approaches to account for within-subject variation, yet only a small number of microbiota studies have applied hierarchical regression models. In this paper, we describe and illustrate the use of a hierarchical regression-based approach to evaluate multiple factors for a small number of organisms individually. More specifically, the zero-inflated negative binomial mixed model with random effects in both the count and zero-inflated parts is applied to evaluate associations with disease state while adjusting for potential confounders for two organisms of interest from a study of human microbiota sequence data in oesophagitis.

Inhibition of interferon-gamma expression by osmotic shrinkage of peripheral blood lymphocytes.

A hypertonic environment, as it prevails in renal medulla or in hyperosmolar states such as hyperglycemia of diabetes mellitus, has been shown to impair the immune response, thus facilitating the development of infection. The present experiments were performed to test whether hypertonicity influences activation of T lymphocytes. To this end, peripheral blood lymphocytes (PBL) of cytomegalovirus (CMV)-positive donors were stimulated by human leukocyte antigen (HLA)-A2-restricted CMV epitope NLVPMVATV to produce interferon (IFN)-gamma at varying extracellular osmolarity. As a result, increasing extracellular osmolarity during exposure to the CMV antigen indeed decreased IFN-gamma formation. Addition of NaCl was more effective than urea. A 50% inhibition was observed at 350 mosM by addition of NaCl. The combined application of the Ca(2+) ionophore ionomycin (1 microg/ml) and the phorbol ester phorbol 12-myristate 13-acetate (PMA; 5 microg/ml) stimulated IFN-gamma production, an effect again reversed by hyperosmolarity. Moreover, hyperosmolarity abrogated the stimulating effect of ionomycin (1 microg/ml) and PMA (5 microg/ml) on the transcription factors activator protein (AP)-1, nuclear factor of activated T cells (NFAT), and NF-kappaB but not Sp1. In conclusion, osmotic cell shrinkage blunts the stimulatory action of antigen exposure on IFN-gamma production, an effect explained at least partially by suppression of transcription factor activation.

K+ channel activation by all three isoforms of serum- and glucocorticoid-dependent protein kinase SGK.

The serum- and glucocorticoid-dependent kinase SGK1 was originally identified as a glucocorticoid-sensitive gene. Subsequently, the two homologous kinases SGK2 and SGK3 have been cloned, being products of distinct genes, which are differentially expressed and share 80% identity in amino acid sequence in their catalytic domains. While SGK1 has been shown to activate ion channels, including K(+) channels, the functions of SGK2 and SGK3 have not been examined. The present study was therefore performed to elucidate the effect of SGK1, SGK2, and SGK3 on electrical properties of renal epithelial cells. To this end human embryonic kidney (HEK293) cells were transfected with the kinases and ion-channel activity determined using the patch-clamp technique. In non-transfected cells and in cells transfected with the empty GFP construct a voltage-gated K(+) current was observed amounting to 303+/-19 pA ( n=13) and 299+/-29 pA ( n=23), respectively. Transfection with SGK1, SGK2 or SGK3 increased the voltage-gated K(+) current to 1056+/-152 pA ( n=17), 555+/-47 pA ( n=17), and 775+/-98 pA ( n=16), respectively. The K(+) current was fully blocked by 3 mM tetraethylammonium chloride and inhibited 45% by the Kv1 channel blocker margatoxin (10 nM). In dual electrode voltage-clamp experiments SGK isoforms up-regulated Kv1 voltage-gated K(+)channels expressed in Xenopus laevis oocytes. The present observations thus reveal a powerful stimulating effect of all three isoforms of SGK on K(+) channels. Those effects may participate in regulation of epithelial transport, cell proliferation, and neuromuscular excitability.

Time-dependent regulation of capacitative Ca2+ entry by IGF-1 in human embryonic kidney cells.

In a wide variety of cells, mitogenic factors release Ca(2+) from intracellular stores. The fall of the [Ca(2+)] within the lumen of the Ca(2+)-storing organelles triggers in many cells capacitative Ca(2+) entry (CCE). The present study was performed to elucidate the effect of insulin-like growth factor (IGF-1) on CCE in human embryonic kidney (HEK 293) cells. After depletion of Ca(2+) stores by thapsigargin, CCE was assessed by the increase in cytosolic free [Ca(2+)] (Fura-2 fluorescence imaging) when raising extracellular [Ca(2+)] from 0 to physiological concentrations. IGF-1 exposure (50 ng/ml) for 4 h in serum-free medium markedly enhanced CCE, while a 24-h exposure to IGF-1 depressed CCE profoundly. As some Ca(2+) channels are highly sensitive to the cell membrane potential, and as IGF-1 has been reported to enhance K(+) channel activity, the influence of K(+) channel blockers on the IGF-1-dependent stimulation of CCE was also tested. TEA, charybdotoxin and margatoxin decreased CCE. Similar to the total capacitative calcium entry, the fraction of CCE that was sensitive to K(+) channel blockers was increased after 4 h and decreased after 24 h exposure to IGF-1. Taken together, these data suggest that IGF-1 induces a transient increase followed by a decrease of CCE, and that these effects are at least partly dependent on IGF-1-induced K(+) channel activity.

IGF-1 up-regulates K+ channels via PI3-kinase, PDK1 and SGK1.

Involvement of voltage-gated (Kv) potassium channels in IGF-1-induced proliferation of HEK293 cells was studied by patch-clamp, RT-PCR and FACS analysis. IGF-1 up-regulated outwardly rectifying whole-cell K+ current starting after 1 h of incubation and reaching a maximum after 4-6 h. The IGF-1-stimulated current was voltage-gated with an activation threshold of -30 mV to -40 mV, a half-maximal activation at +5.3+/-1.8 mV, and time constants for activation and inactivation of 4.5+/-0.4 ms and 43.5+/-5.6 ms ( n=10), respectively. The current was inhibited by TEA, margatoxin, agitoxin-2 and stichodactyla toxin. PCR amplification of different Kv subunits from HEK293 cDNA demonstrated the expression of Kv1.1, Kv1.2, Kv1.3, Kv1.4, Kv3.1 and Kv3.4 mRNA. Quantitative RT-PCR showed up-regulation of Kv1.1, 1.2 and 1.3 mRNA by IGF-1. The effect of IGF-1 on K+ current was blocked by inhibitors of phosphatidylinositol 3-kinase (PI3-kinase), wortmannin and LY294002, and mimicked by overexpression of human 3-phosphoinositide-dependent protein kinase-1 (hPDK1) or serum- and glucocorticoid-dependent kinase-1 (hSGK1), both sequential downstream targets of PI3-kinase. IGF-1-induced proliferation of HEK293 cells was inhibited by both K+ channel blockers and inhibitors of PI3-kinase. In conclusion, IGF-1 through PI3-kinase, PDK1 and SGK1 up-regulates Kv channels, an effect required for the proliferative action of the growth factor.

Stimulation of TNF alpha expression by hyperosmotic stress.

Hyperosmotic stress is known to induce apoptotic cell death, an effect previously attributed to seemingly ligand-independent clustering of tumour necrosis factor alpha (TNF alpha) receptors. An alternative explanation for the clustering of TNF alpha receptors may be stimulation of TNF alpha production, with subsequent autocrine or paracrine stimulation of the receptors. The present study was performed to test for an effect of exposure to hyperosmotic extracellular fluid on cellular TNF alpha production. In both the macrophage cell line U937 and the B lymphocyte cell line LCL721, an increase of extracellular osmolarity to 500 mosmol/l indeed increased TNF alpha expression, an effect reversed by the p38 kinase inhibitor SB203580. In both cell types hyperosmotic stress triggered apoptosis, which in U937 cells was significantly inhibited by neutralizing antibodies against TNF alpha and by SB203580 and was similarly elicited by exogenous addition of TNF alpha. In contrast, osmotically induced apoptosis of LCL721 cells was only slightly blunted by anti-TNF alpha antibodies and rather increased by SB203580. In conclusion, through activation of p38 kinase hyperosmotic stress stimulates the expression of TNF alpha which at least in U937 macrophages may participate in the triggering of subsequent apoptotic cell death. However, the observations in LCL721 cells point to other, TNF alpha-independent, mechanisms mediating apoptotic cell death following an excessive increase of extracellular osmolarity.

Association of 4F2hc with light chains LAT1, LAT2 or y+LAT2 requires different domains.

Heterodimeric amino acid transporters are comprised of a type-II membrane protein named the heavy chain (4F2hc or rBAT) that may associate with a number of different polytopic membrane proteins, called light chains. It is thought that the heavy chain is mainly involved in the trafficking of the complex to the plasma membrane, whereas the transport process itself is catalysed by the light chain. The 4F2 heavy chain (4F2hc) associates with at least six different light chains to induce distinct amino acid-transport activites. To test if the light chains are specifically recognized and to identify domains involved in the recognition of light chains, C-terminally truncated mutants of 4F2hc were constructed and co-expressed with the light chains LAT1, LAT2 and y(+)LAT2. The truncated isoform T1, comprised of only 133 amino acids that form the cytosolic N-terminus and the transmembrane helix, displayed only a slight reduction in its ability to promote LAT1 expression at the membrane surface compared with the 529 amino acid wild-type 4F2hc protein. Co-expression of increasingly larger 4F2hc mutants caused a delayed translocation of LAT1. In contrast to the weak effects of 4F2hc truncations on LAT1 expression, surface expression of LAT2 and y(+)LAT2 was almost completely lost with all truncated heavy chains. Co-expression of LAT1 together with the other light chains did not result in displacement of LAT2 and y(+)LAT2. The results suggest that extracellular domains of the heavy chain are responsible mainly for recognition of light chains other than LAT1 and that the extracellular domain ensures proper translocation to the plasma membrane.

Serum- and glucocorticoid-dependent kinase, cell volume, and the regulation of epithelial transport.

Ample pharmacological evidence points to a role of kinases in the regulation of cell volume. Given the limited selectivity of most inhibitors, however, the specific molecules involved have remained largely elusive. The search for cell volume regulated genes in liver HepG2 cells led to the discovery of the human serum- and glucocorticoid-dependent serine/threonine kinase hsgk1. Transcription and expression of hsgk1 is markedly and rapidly upregulated by osmotic and isotonic cell shrinkage. The effect of osmotic cell shrinkage on hsgk1 is mediated by p38 kinase. Further stimuli of hsgk1 transcription include glucocorticoids, aldosterone, TGF-beta1, serum, increase of intracellular Ca2+ and phorbolesters, whereas cAMP downregulates hsgk1 transcription. The hsgk1 protein is expressed in several epithelial tissues including human pancreas, intestine, kidney, and shark rectal gland. Co-expression of hsgk1 with the renal epithelial Na+-channel ENaC or the Na+/K+/2Cl(-)-cotransporter NKCC2 (BSC1) in Xenopus oocytes, accelerates insertion of the transport proteins into the cell membrane and thus, stimulates channel or transport activity. Thus, hsgk1 participates in the regulation of transport by steroids and secretagogues increasing intracellular Ca2+-activity. The stimulation of hsgk1 transcription by TGF-beta1 may further bear pathophysiological relevance.

Cell volume in the regulation of cell proliferation and apoptotic cell death.

Cell proliferation must - at some time point - lead to increase of cell volume and one of the hallmarks of apoptosis is cell shrinkage. At constant extracellular osmolarity those alterations of cell volume must reflect respective changes of cellular osmolarity which are hardly possible without the participation of cell volume regulatory mechanisms. Indeed, as shown for ras oncogene expressing 3T3 fibroblasts, cell proliferation is paralleled by activation of Na(+)/H(+) exchange and Na(+),K(+),2Cl(-) cotransport, the major transport systems accomplishing regulatory cell volume increase. Conversely, as evident from CD95-induced apoptotic cell death, apoptosis is paralleled by inhibition of Na(+)/H(+) exchanger and by activation of Cl(-) channels and release of the organic osmolyte taurine, major components of regulatory cell volume decrease. However, ras oncogene activation leads to activation and CD95 receptor triggering to inhibition of K(+) channels. The effects counteract the respective cell volume changes. Presumably, they serve to regulate cell membrane potential, which is decisive for Ca(++) entry through I(CRAC) and the generation of cytosolic Ca(++) oscillations in proliferating cells. As a matter of fact I(CRAC) is activated in ras oncogene expressing cells and inhibited in CD95-triggered cells. Activation of K(+) channels and Na(+)/H(+) exchanger as well as Ca(++) oscillations have been observed in a wide variety of cells upon exposure to diverse mitogenic factors. Conversely, diverse apoptotic factors have been shown to activate Cl(-) channels and organic osmolyte release. Inhibition of K(+) channels is apparently, however, not a constant phenomenon paralleling apoptosis which in some cells may even require the operation of K(+) channels. Moreover, cell proliferation may at some point require activation of Cl(-) channels. In any case, the alterations of cell volume are obviously important for the outcome, as cell shrinkage impedes cell proliferation and apoptosis can be elicited by increase of extracellular osmolarity. At this stage little is known about the interplay of cell volume regulatory mechanisms and the cellular machinery leading to mitosis or death of the cell. Thus, considerable further experimental effort is required in this exciting area of cell physiology.

h-sgk serine-threonine protein kinase as transcriptional target of p38/MAP kinase pathway in HepG2 human hepatoma cells.

The human serum and glucocorticoid dependent serine/threonine kinase h-sgk has previously been discovered as cell volume regulated gene. The present study has been performed to elucidate the involvement of p38-kinase in the transcriptional control of h-sgk by osmotic cell shrinkage. The p38-kinase has previously been cloned as the mammalian homologue of HOG1 kinase, which constitutes a part of the osmosensor in the yeast Saccharomyces cerevisiae. Phosphorylated (active) p38-kinase has been estimated with Western blotting, transcription of hsgk using Northern blotting. Both, increase of extracellular NaCl concentration by 50 mmol/l and addition of 10 micromol/l anisomycin increase phosphorylation of the p38-kinase within 5 to 10 minutes. h-sgk transcription is upregulated by addition of 50 mmol/l NaCl and by anisomycin (10 micromol/l), effects completely inhibited by the specific p38-kinase inhibitor, SB 203580 (10 micromol/l). In conclusion, the stimulation of h-sgk transcription by osmotic cell shrinkage is mediated by p38-kinase.

Neutralization of measles virus wild-type isolates after immunization with a synthetic peptide vaccine which is not recognized by neutralizing passive antibodies.

The sequence H379-410 of the measles virus haemagglutinin (MV-H) protein forms a surface-exposed loop and contains three cysteine residues (Cys-381, Cys-386 and Cys-394) which are conserved among all measles isolates. It comprises the minimal sequential B cell epitope (BCE) (H386-400) of the neutralizing and protective MAb BH6 that neutralizes all wild-type viruses tested. The aim of this study was to design synthetic peptides which induce neutralizing antibodies against MV wild-type isolates. Peptides containing one or two copies of T cell epitopes (TCE) and BCEs of different lengths (H386-400, B(CC); H379-400, B(CCC)), in different combinations and orientations were produced and iteratively optimized for inducing neutralizing antibodies. Peptides with the shorter BCE induced sera that cross-reacted with MV but did not neutralize. The longer BCE containing the three cysteines (B(CCC)) and two homologous TCE were required for neutralization activity. These sera neutralized wild-type strains of different clades and geographic origins. Neutralizing serum was also obtained after immunization with human promiscuous TCEs. Furthermore B(CCC)-based peptides were fully immunogenic even in the presence of pre-existing MV-specific antibodies. The results suggest that subunit vaccines based on such peptides could potentially be used to actively protect infants against wild-type viruses irrespective of persisting maternal antibodies.

Analysis of a hepatitis delta virus isolate from the Central African Republic.

Based on the analysis of HDV genomes from different areas of the world, three genotypes of HDV have been identified. Genotype I is the most prevalent and widespread. Genotype II is represented by two isolates from Japan and Taiwan. Genotype III has been found only in the Amazonian basin where it is associated with a history of severe disease, fulminant hepatitis with microvesicular steatosis (spongiocytosis). We report here the cloning and the analysis of the complete viral genome from woodchuck serum-derived HDV RNA after transmission from Central African Republic (RCA) patients with fulminant spongiocytic delta hepatitis. Two overlapping cDNA fragments, covering the entire HDV genome, were generated by RT-PCR and cloned. Three clones obtained from each fragment were fully sequenced. A complete consensus RCA HDV genome was reconstituted. The individual and the consensus nucleotide sequences were compared with those of 16 other fully sequenced isolates belonging to the three genotypes. Phylogenetic trees generated by the neighbour joining method firmly place our isolate in genotype I, and show that this RCA isolate differs significantly from the east African isolates previously analysed. Transfection experiments showed that the isolate is replication-competent, but less so than the control "wild-type" strain. Two novel mutations encountered in this work, one in the antigenomic ribozyme sequence and one affecting delta antigen, were studied.

Zidovudine treatment is not associated with HTLV-1 reverse transcriptase gene mutations in HTLV-I/HIV-1 co-infected patients.

Zidovudine treatment of human immunodeficiency virus (HIV) infection induces drug-resistant viral strains harbouring specific amino acid substitutions in the reverse transcriptase (RT). To investigate whether this phenomenon could be observed in the case of human T lymphotropic virus type I (HTLV-I) infection, we analysed the HTLV-I RT proviral gene sequence in five HTLV-I/HIV-1 co-infected patients treated with zidovudine for HIV-1 infection and in one untreated co-infected subject. In the 816 bp of HTLV-I pol gene sequence determined, no particular nucleotide mutation associated with zidovudine therapy could be identified in the treated subjects. Moreover, the dominant HTLV-1 deduced amino acid sequences determined in treated subjects were identical to that from the untreated subject. Our data show that in the co-infected patients already presenting well-defined mutations associated with zidovudine resistance in HIV-1, no mutations were observed in a part of the pol gene coding for the RT activity of HTLV-I.

In vivo and in vitro sequence diversity of the V3 env region of HIV type 1 from the Ivory Coast.

PIP: Nine divergent clades of HIV-1 have been detected in Africa, indicating a far greater genetic diversity of the virus on the continent relative to elsewhere in the world. The envelope of HIV-1, especially the V3 loop, which is implicated in viral tropism and in the neutralizing domain, is considered to be a major target for vaccine research. The authors analyzed proviral DNA and RNA viral sequences of the V3 region of the env gene obtained from the plasma and lymphocytes of six people with AIDS originating from the Ivory Coast. The four men and two women exhibited clinical AIDS and pulmonary tuberculosis. The inferred amino acid sequence of the V3 region derived from the DNA sequences obtained in the study were aligned together with the reference sequence of subtype A from the Los Alamos HIV sequence database. The identity of the conserved tetrapeptide motif at the tip of the V3 loop in all the isolates is GPGQ and is consistent with the common motif sequence found in the database for the A subtype. The major changes in the amino acids are localized in the flanking sequences of the V3 loop. The V3 loop of HIV isolates from patient CI-39 presents a change of D to R in position 25, associated with an unusual change in position 24 of G to D. These mutations were found in both viral RNA sequences and in the proviral DNA sequences from uncultured peripheral mononuclear cells (PBMCs), possibly reflecting an infectious viral variant which is actively expressed in vivo and present in plasma. The change of an acidic amino acid to a basic amino acid at position 25 appears to be an important viral tropism determinant.^ieng