The differential effects of PGE on the immune response in normal and immunosuppressed mice

The effect of 16,16-dimethyl-PGE₂-methyl ester (di-M-PGE₂) on humoral and cellular immunoresponsiveness has been compared in normal mice and in mice immunosuppressed by splenectomy and thymectomy plus antithymocyte serum (ATS). Splenectomy resulted in immunosuppression manifested by augmentation of B-16 melanoma growth; this stimulatory effect was reversed by di-M-PGE₂. In animals immunosuppressed by thymectomy plus ATS, di-M-PGE₂ augmented the humoral and cellular immune responses; this was manifested by slowing of the growth of B-16 melanoma and by stimulating the number of plaque-forming cells, hemagglutinin titers, and delayed-hypersensitivity reactions to sheep erythrocytes. In contrast, in normal (nonthymectomized) mice, di-M-PGE₂ was mildly immunosuppressive. Finally, adriamycin-immunosuppressed normal mice and this suppression were reversed by the addition of di-M-PGE₂ to the treatment regimen.     

Cytoplasmic targeting of mutant poly(A)-binding protein nuclear 1 suppresses protein aggregation and toxicity in oculopharyngeal muscular dystrophy

Oculopharyngeal muscular dystrophy (OPMD) is an adult-onset disorder characterized by progressive eyelid drooping, swallowing difficulties and proximal limb weakness. The autosomal dominant form of this disease is caused by a polyalanine expansion from 10 to 12-17 residues, located at the N-terminus of the poly(A)-binding protein nuclear 1 (PABPN1). A distinct pathological hallmark of OPMD is the presence of filamentous intranuclear aggregates in patients' skeletal muscle cells. Wildtype PABPN1 protein is expressed ubiquitously and was shown to be mostly concentrated in discrete nuclear domains called 'speckles'. Using an established cell- culture model, we show that most mutant PABPN1- positive (alanine expanded form) intranuclear aggregates are structures distinct from intranuclear speckles. In contrast, the promyelocytic leukaemia protein, a major component of nuclear bodies, strongly colocalized to intranuclear aggregates of mutant PABPN1. Wildtype PABPN1 can freely shuttle between the nucleus and cytoplasm. We determined whether the nuclear environment is necessary for mutant PABPN1 inclusion formation and cellular toxicity. This was achieved by inactivating the mutant PABPN1 nuclear localization signal and by generating full-length mutant PABPN1 fused to a strong nuclear export sequence. A green fluorescence protein tag inserted at the N-terminus of both wildtype PABPN1 (ala10) and mutant PABPN1 (ala17) proteins allowed us to visualize their subcellular localization. Targeting mutant PABPN1 to the cytoplasm resulted in a significant suppression of both intranuclear aggregates formation and cellular toxicity, two histological consequences of OPMD. Our results indicate that the nuclear localization of mutant PABPN1 is crucial to OPMD pathogenesis.     

The α promoter regulator-ovalbumin chimeric gene resident in human cells is regulated like the authentic α 4 gene after infection with herpes simplex virus 1 mutants in α 4 gene

Human TK^? 143 cells were converted to TK⁺ phenotype with a plasmid containing the native herpes simplex virus 1 (HSV-1), thymidine kinase, a β gene, and a chimeric ovalbumin gene consisting of the coding sequences of the ovalbumin gene linked to the promoter-regulatory region of the HSV-1 α 4 gene. Comparison of the synthesis of ovalbumin and the α 4 gene product in the converted cells infected with ts mutants in α 4 gene and incubated at the permissive (33°C) and nonpermissive (39°C) temperatures revealed the following. (i) The synthesis of both ovalbumin and α 4 gene product was transiently induced at the permissive temperature but continued at elevated levels for many hours at the nonpermissive temperature. (ii) The synthesis of both ovalbumin and α 4 gene products resumed when the infected cells were shifted from permissive to nonpermissive temperature after the shut-off of α protein synthesis. (iii) Although both the β-TK and α 4-ovalbumin chimeric genes were covalently linked on the same plasmid, each was regulated independently. We conclude that α gene regulation is determined solely by (a) the inducer and (b) the induction sequence contained in the promoter-regulatory region and not by the location or the higher order structure of the immediate environment of the gene.     

Toward a more holistic ecology,and science: the contribution of H.T. Odum

Conclusion For the abovementioned reasons, and with all due respect to the scholarship of Mansson and McGlade, who display a deep knowledge of thermodynamics and ecology, I cannot agree that Odum's use of energy concepts is wholly discredited. Refinements from microscopic thermodynamics may not have been faithfully carried along in his work, but does ecology really need these? Remember — the meal test.Having tussled with ecological complexity myself, I stand in awe of this man who has faced up to what most ecologists today are trying to deny — intractable, crushing, defeating complexity. If Odum has provided some of the first shaky stepping stones across this gulf, that's enough.I can finish by quoting from ny Festschrift paper again:It is often said of scientists who make unusual contributions against the grain of their disciplines that they are ahead of their time. In H.T. Odum's case, with maximum power, energy-circuit diagrams, emergy, transformity, and energy value the linchpins of a whole new theory of ecology, and paradigm within systems ecology, this can certainly be stated without hesitation. But in this instance, it is also possible to turn the observation around and suggest that ecology-as-science is behind its time, lagging the curve of need foreseen decades ago by a more pragmatic ecology-as-ethic and-concern. The growing man-and-environment tension, fostered by so-far unabatable growth of populations, technologies and economies, demands a science that incises complexity, finds the essence of systemness, and produces quantitative methods capable of moulding this essence to meet the imperatives of the new environmentalism. H.T. Odum has not, perhaps, provided a definitive theory to do this; no one could right now. But, he has given us an intriguing mix of science, art and religion that stands as one of the singular legacies of 20th-century ecology, pointing the way toward a new ecology of complexity that must, I think from need, fully arise in the 21st century. His time has been behind him.     

Plant functional traits capture species richness variations along a flooding gradient

Local species coexistence is the outcome of abiotic and biotic filtering processes which sort species according to their trait values. However, the capacity of trait‐based approaches to predict the variation in realized species richness remains to be investigated. In this study, we asked whether a limited number of plant functional traits, related to the leaf‐height‐seed strategy scheme and averaged at the community level, is able to predict the variation in species richness over a flooding disturbance gradient. We further investigated how these mean community traits are able to quantify the strength of abiotic and biotic processes involved in the disturbance–productivity–diversity relationship. We thus tested the proposal that the deviation between the fundamental species richness, assessed from ecological niche‐based models, and realized species richness, i.e. field‐observed richness, is controlled by species interactions. Flooding regime was determined using a detailed hydrological model. A precise vegetation sampling was performed across 222 quadrats located throughout the flooding gradient. Three core functional traits were considered: specific leaf area (SLA), plant height and seed mass. Species richness showed a hump‐shaped response to disturbance and productivity, but was better predicted by only two mean community traits: SLA and height. On the one hand, community SLA that increased with flooding, controlled the disturbance‐diversity relationship through habitat filtering. On the other hand, species interactions, the strength of which was captured by community height values, played a strong consistent role throughout the disturbance gradient by reducing the local species richness. Our study highlights that a limited number of simple, quantitative, easily measurable functional traits can capture the variation in plant species richness at a local scale and provides a promising quantification of key community assembly mechanisms.     

Tomato contains two differentially expressed genes encoding B-type phytochromes,neither of which can be considered an ortholog of Arabidopsis phytochrome B

Tomato (Solanum lycopersicon L.) contains two B-type phytochrome genes (PHYB1 and PHYB2). Fragments of these two PHYB were cloned following amplification by the polymerase chain reaction of a portion of their relatively well conserved 5 coding regions. Polypeptides encoded by these gene fragments exhibit 90% sequence identity. These two PHYB are independently expressed in organ-specific fashion. In mature plants, PHYB2 mRNA is most abundant in fruit and PHYB1 mRNA in expanded leaves. A phylogenetic analysis fails to establish which tomato PHYB is orthologous to either Arabidopsis PHYB or PHYD, the latter being a second B-type phytochrome. Instead, this analysis indicates that following the divergence of the Solanaceae and Brassicaceae from one another, a PHYB gene duplicated independently in each lineage. Consequently, Arabidopsis PHYB mutants cannot be considered strictly equivalent to the tomato tri mutants, which appear to be mutated at the PHYB1 locus. Similarly, other putative PHYB mutants might not be equivalent to those described for Arabidopsis and tomato. This situation complicates efforts to determine PHYB function because there might be no one answer to this question.Abbreviations PCR polymerase chain reaction - PHY undesignated phytochrome gene - PHYA, PHYB, etc phytochrome gene(s) of the A, B, etc. type This research was supported by USDA NRICGP grant 93-00939 and by NATO travel grant CRG 931183. It was initiated when two of us (L.H.P., M.-M.C.-P.) spent a sabbatical year at the Institut National de la Recherche Agronomique in Versailles, France. L.H.P. gratefully acknowledges support provided by a senior guest fellowship from the Ministère de l'enseignement superieur et de la recherche during his stay in Versailles. L.H.P. and M.-M.C.-P thank all of their colleagues in Versailles for their warm hospitality and their willingness to share their expertise with us. We also thank Russell Malmberg, Richard Meagher and Robert Price for helpful discussions concerning the interpretation of molecular phylogenies.     

Studying the Effects of Reproductive Hormones and Bacterial Vaginosis on the Glycome of Lavage Samples from the Cervicovaginal Cavity

The cervicovaginal fluid (CVF) coating the vaginal epithelium is an important immunological mediator, providing a barrier to infection. Glycosylation of CVF proteins, such as mucins, IgG and S-IgA, plays a critical role in their immunological functions. Although multiple factors, such as hormones and microflora, may influence glycosylation of the CVF, few studies have examined their impact on this important immunological fluid. Herein we analyzed the glycosylation of cervicovaginal lavage (CVL) samples collected from 165 women under different hormonal conditions including: (1) no contraceptive, post-menopausal, (2) no contraceptive, days 1-14 of the menstrual cycle, (3) no contraceptive, days 15-28 of the menstrual cycle, (4) combined-oral contraceptive pills for at least 6 months, (5) depo-medroxyprogesterone acetate (Depo-Provera) injections for at least 6 months, (6) levonorgestrel IUD for at least 1 month. Glycomic profiling was obtained using our lectin microarray system, a rapid method to analyze carbohydrate composition. Although some small effects were observed due to hormone levels, the major influence on the glycome was the presence of an altered bacterial cohort due to bacterial vaginosis (BV). Compared to normal women, samples from women with BV contained lower levels of sialic acid and high-mannose glycans in their CVL. The change in high mannose levels was unexpected and may be related to the increased risk of HIV-infection observed in women with BV, as high mannose receptors are a viral entry pathway. Changes in the glycome were also observed with hormonal contraceptive use, in a contraceptive-dependent manner. Overall, microflora had a greater impact on the glycome than hormonal levels, and both of these effects should be more closely examined in future studies given the importance of glycans in the innate immune system.     

A new method for class prediction based on signed-rank algorithms applied to Affymetrix<Superscript>®</Superscript> microarray experiments

Background

The huge amount of data generated by DNA chips is a powerful basis to classify various pathologies. However, constant evolution of microarray technology makes it difficult to mix data from different chip types for class prediction of limited sample populations. Affymetrix^® technology provides both a quantitative fluorescence signal and a decision (detection call: absent or present) based on signed-rank algorithms applied to several hybridization repeats of each gene, with a per-chip normalization. We developed a new prediction method for class belonging based on the detection call only from recent Affymetrix chip type. Biological data were obtained by hybridization on U133A, U133B and U133Plus 2.0 microarrays of purified normal B cells and cells from three independent groups of multiple myeloma (MM) patients.

Results

After a call-based data reduction step to filter out non class-discriminative probe sets, the gene list obtained was reduced to a predictor with correction for multiple testing by iterative deletion of probe sets that sequentially improve inter-class comparisons and their significance. The error rate of the method was determined using leave-one-out and 5-fold cross-validation. It was successfully applied to (i) determine a sex predictor with the normal donor group classifying gender with no error in all patient groups except for male MM samples with a Y chromosome deletion, (ii) predict the immunoglobulin light and heavy chains expressed by the malignant myeloma clones of the validation group and (iii) predict sex, light and heavy chain nature for every new patient. Finally, this method was shown powerful when compared to the popular classification method Prediction Analysis of Microarray (PAM).

Conclusion

This normalization-free method is routinely used for quality control and correction of collection errors in patient reports to clinicians. It can be easily extended to multiple class prediction suitable with clinical groups, and looks particularly promising through international cooperative projects like the "Microarray Quality Control project of US FDA" MAQC as a predictive classifier for diagnostic, prognostic and response to treatment. Finally, it can be used as a powerful tool to mine published data generated on Affymetrix systems and more generally classify samples with binary feature values.