From data to discovery: AI-guided analysis of disease-relevant molecules in spinal muscular atrophy (SMA)

Spinal Muscular Atrophy is caused by partial loss of survival of motoneuron (SMN) protein expression. The numerous interaction partners and mechanisms influenced by SMN loss result in a complex disease. Current treatments restore SMN protein levels to a certain extent, but do not cure all symptoms. The prolonged survival of patients creates an increasing need for a better understanding of SMA. Although many SMN-protein interactions, dysregulated pathways, and organ phenotypes are known, the connections among them remain largely unexplored. Monogenic diseases are ideal examples for the exploration of cause-and-effect relationships to create a network describing the disease-context. Machine learning tools can utilize such knowledge to analyze similarities between disease-relevant molecules and molecules not described in the disease so far. We used an artificial intelligence-based algorithm to predict new genes of interest. The transcriptional regulation of 8 out of 13 molecules selected from the predicted set were successfully validated in an SMA mouse model. This bioinformatic approach, using the given experimental knowledge for relevance predictions, enhances efficient targeted research in SMA and potentially in other disease settings.

bootGSEA: a bootstrap and rank aggregation pipeline for multi-study and multi-omics enrichment analyses

Introduction: Gene set enrichment analysis (GSEA) subsequent to differential expression analysis is a standard step in transcriptomics and proteomics data analysis. Although many tools for this step are available, the results are often difficult to reproduce because set annotations can change in the databases, that is, new features can be added or existing features can be removed. Finally, such changes in set compositions can have an impact on biological interpretation. Methods: We present bootGSEA, a novel computational pipeline, to study the robustness of GSEA. By repeating GSEA based on bootstrap samples, the variability and robustness of results can be studied. In our pipeline, not all genes or proteins are involved in the different bootstrap replicates of the analyses. Finally, we aggregate the ranks from the bootstrap replicates to obtain a score per gene set that shows whether it gains or loses evidence compared to the ranking of the standard GSEA. Rank aggregation is also used to combine GSEA results from different omics levels or from multiple independent studies at the same omics level. Results: By applying our approach to six independent cancer transcriptomics datasets, we showed that bootstrap GSEA can aid in the selection of more robust enriched gene sets. Additionally, we applied our approach to paired transcriptomics and proteomics data obtained from a mouse model of spinal muscular atrophy (SMA), a neurodegenerative and neurodevelopmental disease associated with multi-system involvement. After obtaining a robust ranking at both omics levels, both ranking lists were combined to aggregate the findings from the transcriptomics and proteomics results. Furthermore, we constructed the new R-package "bootGSEA," which implements the proposed methods and provides graphical views of the findings. Bootstrap-based GSEA was able in the example datasets to identify gene or protein sets that were less robust when the set composition changed during bootstrap analysis. Discussion: The rank aggregation step was useful for combining bootstrap results and making them comparable to the original findings on the single-omics level or for combining findings from multiple different omics levels.

Renal pathology in a mouse model of severe Spinal Muscular Atrophy is associated with downregulation of Glial Cell-Line Derived Neurotrophic Factor (GDNF)

Spinal muscular atrophy (SMA) occurs as a result of cell-ubiquitous depletion of the essential survival motor neuron (SMN) protein. Characteristic disease pathology is driven by a particular vulnerability of the ventral motor neurons of the spinal cord to decreased SMN. Perhaps not surprisingly, many other organ systems are also impacted by SMN depletion. The normal kidney expresses very high levels of SMN protein, equivalent to those found in the nervous system and liver, and levels are dramatically lowered by ~90-95% in mouse models of SMA. Taken together, these data suggest that renal pathology may be present in SMA. We have addressed this using an established mouse model of severe SMA. Nephron number, as assessed by gold standard stereological techniques, was significantly reduced. In addition, morphological assessment showed decreased renal vasculature, particularly of the glomerular capillary knot, dysregulation of nephrin and collagen IV, and ultrastructural changes in the trilaminar filtration layers of the nephron. To explore the molecular drivers underpinning this process, we correlated these findings with quantitative PCR measurements and protein analyses of glial cell-line-derived neurotrophic factor, a crucial factor in ureteric bud branching and subsequent nephron development. Glial cell-line-derived neurotrophic factor levels were significantly reduced at early stages of disease in SMA mice. Collectively, these findings reveal significant renal pathology in a mouse model of severe SMA, further reinforcing the need to develop and administer systemic therapies for this neuromuscular disease.

The Senescence-associated Secretory Phenotype Mediates Oncogene-induced Senescence in Pediatric Pilocytic Astrocytoma

PURPOSE

Pilocytic astrocytoma is the most common childhood brain tumor, characterized by constitutive MAPK activation. MAPK signaling induces oncogene-induced senescence (OIS), which may cause unpredictable growth behavior of pilocytic astrocytomas. The senescence-associated secretory phenotype (SASP) has been shown to regulate OIS, but its role in pilocytic astrocytoma remains unknown.Experimental Design: The patient-derived pilocytic astrocytoma cell culture model, DKFZ-BT66, was used to demonstrate presence of the SASP and analyze its impact on OIS in pilocytic astrocytoma. The model allows for doxycycline-inducible switching between proliferation and OIS. Both states were studied using gene expression profiling (GEP), Western blot, ELISA, and cell viability testing. Primary pilocytic astrocytoma tumors were analyzed by GEP and multiplex assay.

RESULTS

SASP factors were upregulated in primary human and murine pilocytic astrocytoma and during OIS in DKFZ-BT66 cells. Conditioned medium induced growth arrest of proliferating pilocytic astrocytoma cells. The SASP factors IL1B and IL6 were upregulated in primary pilocytic astrocytoma, and both pathways were regulated during OIS in DKFZ-BT66. Stimulation with rIL1B but not rIL6 reduced growth of DKFZ-BT66 cells and induced the SASP. Anti-inflammatory treatment with dexamethasone induced regrowth of senescent cells and inhibited the SASP. Senescent DKFZ-BT66 cells responded to senolytic BCL2 inhibitors. High IL1B and SASP expression in pilocytic astrocytoma tumors was associated with favorable progression-free survival.

CONCLUSIONS

We provide evidence for the SASP regulating OIS in pediatric pilocytic astrocytoma, with IL1B as a relevant mediator. SASP expression could enable prediction of progression in patients with pilocytic astrocytoma. Further investigation of the SASP driving the unpredictable growth of pilocytic astrocytomas, and its possible therapeutic application, is warranted.

Long-Term Visual Outcome of Choroidal Neovascularization in Pathologic Myopia: Natural History and Laser Treatment

This retrospective study was designed to help clarify the visual prognosis during long-term follow-up (5-10 years) of myopic choroidal neovascularization (CNV) with and without laser treatment in a referral population.

Patients and Methods.

A group of 50 consecutive non-treated eyes and a group of 50 consecutive treated eyes were selected retrospectively. Inclusion criteria were: fluorescein angiographic documentation of CNV not involving the center of the fovea, visual acuity (VA) > 20/200, age less than 60, onset of symptoms ≤ 6 months and at least five years of follow-up. The mean decrease in VA in non-treated and treated eyes during the follow-up was analysed on the basis of subgroups with the same initial VA.

Results

Considering both groups (100 eyes) at presentation, 89% of CNV spared the center of the fovea but were located in the foveolar area (< 200 μm) and only 11% were extrafoveal (> 200 μm). In the natural history group, after five years all CNV involved the center of the fovea and mean VA was 20/160. In the treated group, at the end of the five year follow-up and after one or more laser session, 64% of eyes had a dry scar and mean VA was 20/74. Nevertheless there was a very high rate of recurrences (72%) and at the end of follow-up, 36% of treated eyes had a subfoveal recurrence with a mean decrease in VA to 20/154. The difference between the mean decrease in VA of the treated and non-treated groups was statistically significant at two years. At five years (100 eyes), the difference persisted only for eyes with initial VA better than ≥ 20/40 (P<0.05). At eight years (76 eyes) and ten years (24 eyes), this difference was no longer significant.

Comments

This study confirms that CNV accompanying degenerative myopia has an extremely poor prognosis. Nevertheless analysis of final VA in both groups suggests that eyes with high initial VA gain more from treatment.

The differential production cross section of the [Formula: see text](1020) meson in [Formula: see text] = 7 TeV [Formula: see text] collisions measured with the ATLAS detector

A measurement is presented of the [Formula: see text] production cross section at [Formula: see text] = 7 TeV using [Formula: see text] collision data corresponding to an integrated luminosity of 383 [Formula: see text], collected with the ATLAS experiment at the LHC. Selection of [Formula: see text](1020) mesons is based on the identification of charged kaons by their energy loss in the pixel detector. The differential cross section is measured as a function of the transverse momentum, [Formula: see text], and rapidity, [Formula: see text], of the [Formula: see text](1020) meson in the fiducial region 500 [Formula: see text] 1200 MeV, [Formula: see text] 0.8, kaon [Formula: see text] 230 MeV and kaon momentum [Formula: see text] 800 MeV. The integrated [Formula: see text]-meson production cross section in this fiducial range is measured to be [Formula: see text] = 570 [Formula: see text] 8 (stat) [Formula: see text] 66 (syst) [Formula: see text] 20 (lumi) [Formula: see text].

Evidence of promiscuous endothelial binding by Plasmodium falciparum-infected erythrocytes

The adhesion of infected red blood cells (iRBCs) to human endothelium is considered a key event in the pathogenesis of cerebral malaria and other life‐threatening complications caused by the most prevalent malaria parasite Plasmodium falciparum. In the past 30 years, 14 endothelial receptors for iRBCs have been identified. Exposing 10 additional surface proteins of endothelial cells to a mixture of P. falciparum isolates from three Ghanaian malaria patients, we identified seven new iRBC receptors, all expressed in brain vessels. This finding strongly suggests that endothelial binding of P. falciparum iRBCs is promiscuous and may use a combination of endothelial surface moieties.

Improved luminosity determination in pp collisions at [Formula: see text] using the ATLAS detector at the LHC

The luminosity calibration for the ATLAS detector at the LHC during pp collisions at [Formula: see text] in 2010 and 2011 is presented. Evaluation of the luminosity scale is performed using several luminosity-sensitive detectors, and comparisons are made of the long-term stability and accuracy of this calibration applied to the pp collisions at [Formula: see text]. A luminosity uncertainty of [Formula: see text] is obtained for the 47 pb-1 of data delivered to ATLAS in 2010, and an uncertainty of [Formula: see text] is obtained for the 5.5 fb-1 delivered in 2011.

Measurement of the inclusive jet cross-section in pp collisions at [Formula: see text] and comparison to the inclusive jet cross-section at [Formula: see text] using the ATLAS detector

The inclusive jet cross-section has been measured in proton-proton collisions at [Formula: see text] in a dataset corresponding to an integrated luminosity of [Formula: see text] collected with the ATLAS detector at the Large Hadron Collider in 2011. Jets are identified using the anti-kt algorithm with two radius parameters of 0.4 and 0.6. The inclusive jet double-differential cross-section is presented as a function of the jet transverse momentum pT and jet rapidity y, covering a range of 20≤pT<430 GeV and |y|<4.4. The ratio of the cross-section to the inclusive jet cross-section measurement at [Formula: see text], published by the ATLAS Collaboration, is calculated as a function of both transverse momentum and the dimensionless quantity [Formula: see text], in bins of jet rapidity. The systematic uncertainties on the ratios are significantly reduced due to the cancellation of correlated uncertainties in the two measurements. Results are compared to the prediction from next-to-leading order perturbative QCD calculations corrected for non-perturbative effects, and next-to-leading order Monte Carlo simulation. Furthermore, the ATLAS jet cross-section measurements at [Formula: see text] and [Formula: see text] are analysed within a framework of next-to-leading order perturbative QCD calculations to determine parton distribution functions of the proton, taking into account the correlations between the measurements.

Measurement of the [Formula: see text] production cross section in the tau + jets channel using the ATLAS detector

A measurement of the top quark pair production cross section in the final state with a hadronically decaying tau lepton and jets is presented. The analysis is based on proton-proton collision data recorded by the ATLAS experiment at the LHC, with a centre-of-mass energy of 7 TeV. The data sample corresponds to an integrated luminosity of 1.67 fb-1. The cross section is measured to be [Formula: see text] and is in agreement with other measurements and with the Standard Model prediction.

Jet energy resolution in proton-proton collisions at [Formula: see text] recorded in 2010 with the ATLAS detector

The measurement of the jet energy resolution is presented using data recorded with the ATLAS detector in proton-proton collisions at [Formula: see text]. The sample corresponds to an integrated luminosity of 35 pb-1. Jets are reconstructed from energy deposits measured by the calorimeters and calibrated using different jet calibration schemes. The jet energy resolution is measured with two different in situ methods which are found to be in agreement within uncertainties. The total uncertainties on these measurements range from 20 % to 10 % for jets within |y|<2.8 and with transverse momenta increasing from 30 GeV to 500 GeV. Overall, the Monte Carlo simulation of the jet energy resolution agrees with the data within 10 %.

Measurement of Z boson production in Pb-Pb collisions at sqrt[s(NN)]=2.76 TeV with the ATLAS detector

The ATLAS experiment has observed 1995 Z boson candidates in data corresponding to 0.15  nb(-1) of integrated luminosity obtained in the 2011 LHC Pb+Pb run at sqrt[s(NN)]=2.76  TeV. The Z bosons are reconstructed via dielectron and dimuon decay channels, with a background contamination of less than 3%. Results from the two channels are consistent and are combined. Within the statistical and systematic uncertainties, the per-event Z boson yield is proportional to the number of binary collisions estimated by the Glauber model. The elliptic anisotropy of the azimuthal distribution of the Z boson with respect to the event plane is found to be consistent with zero.

Search for dark matter candidates and large extra dimensions in events with a photon and missing transverse momentum in pp collision data at sqrt[s]=7 TeV with the ATLAS detector

Results of a search for new phenomena in events with an energetic photon and large missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV are reported. Data collected by the ATLAS experiment at the LHC corresponding to an integrated luminosity of 4.6 fb(-1) are used. Good agreement is observed between the data and the standard model predictions. The results are translated into exclusion limits on models with large extra spatial dimensions and on pair production of weakly interacting dark matter candidates.

Search for magnetic monopoles in sqrt[s]=7 TeV pp collisions with the ATLAS detector

This Letter presents a search for magnetic monopoles with the ATLAS detector at the CERN Large Hadron Collider using an integrated luminosity of 2.0  fb(-1) of pp collisions recorded at a center-of-mass energy of sqrt[s]=7  TeV. No event is found in the signal region, leading to an upper limit on the production cross section at 95% confidence level of 1.6/ϵ  fb for Dirac magnetic monopoles with the minimum unit magnetic charge and with mass between 200 GeV and 1500 GeV, where ϵ is the monopole reconstruction efficiency. The efficiency ϵ is high and uniform in the fiducial region given by pseudorapidity |η|<1.37 and transverse kinetic energy 600-700<E(kin)sinθ<1400  GeV. The minimum value of 700 GeV is for monopoles of mass 200 GeV, whereas the minimum value of 600 GeV is applicable for higher mass monopoles. Therefore, the upper limit on the production cross section at 95% confidence level is 2 fb in this fiducial region. Assuming the kinematic distributions from Drell-Yan pair production of spin-1/2 Dirac magnetic monopoles, the efficiency is in the range 1%-10%, leading to an upper limit on the cross section at 95% confidence level that varies from 145 fb to 16 fb for monopoles with mass between 200 GeV and 1200 GeV. This limit is weaker than the fiducial limit because most of these monopoles lie outside the fiducial region.

Search for direct top squark pair production in final states with one isolated lepton, jets, and missing transverse momentum in sqrt[s] = 7 TeV pp collisions using 4.7 fb(-10 of ATLAS data

A search is presented for direct top squark pair production in final states with one isolated electron or muon, jets, and missing transverse momentum in proton-proton collisions at sqrt[s] = 7 TeV. The measurement is based on 4.7 fb(-1) of data collected with the ATLAS detector at the LHC. Each top squark is assumed to decay to a top quark and the lightest supersymmetric particle (LSP). The data are found to be consistent with standard model expectations. Top squark masses between 230 GeV and 440 GeV are excluded with 95% confidence for massless LSPs, and top squark masses around 400 GeV are excluded for LSP masses up to 125 GeV.

Search for a supersymmetric partner to the top quark in final states with jets and missing transverse momentum at sqrt[s] = 7 TeV with the ATLAS detector

A search for direct pair production of supersymmetric top squarks (t(1)) is presented, assuming the t(1) decays into a top quark and the lightest supersymmetric particle, χ(1)(0), and that both top quarks decay to purely hadronic final states. A total of 16 (4) events are observed compared to a predicted standard model background of 13.5(-3.6)(+3.7)(4.4(-1.3)(+1.7)) events in two signal regions based on ∫Ldt = 4.7 fb(-1) of pp collision data taken at sqrt[s] = 7 TeV with the ATLAS detector at the LHC. An exclusion region in the t(1) versus χ(1)(0) mass plane is evaluated: 370<m(t)(1)}<465 GeV is excluded for m(χ)(1)(0) ~ 0 GeV while m(t)(1) = 445 GeV is excluded for m(χ)(1)(0) ≤ 50 GeV.

A search for [Formula: see text] resonances with the ATLAS detector in 2.05 fb-1 of proton-proton collisions at [Formula: see text]

A search for top quark pair resonances in final states containing at least one electron or muon has been performed with the ATLAS experiment at the CERN Large Hadron Collider. The search uses a data sample corresponding to an integrated luminosity of 2.05 fb-1, which was recorded in 2011 at a proton-proton centre-of-mass energy of 7 TeV. No evidence for a resonance is found and limits are set on the production cross-section times branching ratio to [Formula: see text] for narrow and wide resonances. For narrow Z' bosons, the observed 95 % Bayesian credibility level limits range from 9.3 pb to 0.95 pb for masses in the range of mZ'=500 GeV to mZ'=1300 GeV. The corresponding excluded mass region for a leptophobic topcolour Z' boson (Kaluza-Klein gluon excitation in the Randall-Sundrum model) is mZ'<880 GeV ([Formula: see text]).

Search for supersymmetry in events with three leptons and missing transverse momentum in √[s]=7 TeV pp collisions with the ATLAS detector

A search for the weak production of charginos and neutralinos decaying to a final state with three leptons (electrons or muons) and missing transverse momentum is presented. The analysis uses 2.06 fb(-1) of √[s]=7 TeV proton-proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with standard model expectations in two signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric and simplified models. For the simplified models, degenerate lightest chargino and next-to-lightest neutralino masses up to 300 GeV are excluded for mass differences from the lightest neutralino up to 300 GeV.

Search for lepton flavour violation in the eμ continuum with the ATLAS detector in [Formula: see text]pp collisions at the LHC

This paper presents a search for the t-channel exchange of an R-parity violating scalar top quark ([Formula: see text]) in the e±μ∓ continuum using 2.1 fb-1 of data collected by the ATLAS detector in [Formula: see text]pp collisions at the Large Hadron Collider. Data are found to be consistent with the expectation from the Standard Model backgrounds. Limits on R-parity-violating couplings at 95 % C.L. are calculated as a function of the scalar top mass ([Formula: see text]). The upper limits on the production cross section for pp→eμX, through the t-channel exchange of a scalar top quark, ranges from 170 fb for [Formula: see text] to 30 fb for [Formula: see text].

Measurement of the ZZ production cross section and limits on anomalous neutral triple gauge couplings in proton-proton collisions at sqrt[s] = 7 TeV with the ATLAS detector

A measurement of the ZZ production cross section in proton-proton collisions at sqrt[s] = 7 TeV using data corresponding to an integrated luminosity of 1.02 fb(-1) recorded by the ATLAS experiment at the LHC is presented. Twelve events containing two Z boson candidates decaying to electrons and/or muons are observed, with an expected background of 0.3 ± 0.3(stat)(-0.3)(+0.4)(syst) events. The cross section measured in a phase-space region with good detector acceptance and for dilepton masses within the range 66 to 116 GeV is σ(ZZ → ℓ+ ℓ- ℓ+ ℓ-)(fid) = 19.4(-5.2)(+6.3)(stat)(-0.7)(+0.9)(syst) ± 0.7(lumi) fb. The resulting total cross section for on-shell ZZ production, σ(ZZ)(tot) = 8.5(-2.3)(+2.7)(stat)(-0.3)(+0.4)(syst) ± 0.3(lumi) pb, is consistent with the standard model expectation of 6.5(-0.2)(+0.3) pb calculated at the next-to-leading order in QCD. Limits on anomalous neutral triple gauge boson couplings are derived.

A key enzyme of the Leloir pathway is involved in pathogenicity of Leptosphaeria maculans toward oilseed rape

Agrobacterium tumefaciens-mediated random insertional mutagenesis was used to investigate pathogenicity determinants in Leptosphaeria maculans. One tagged nonpathogenic mutant, termed m186, is analyzed in detail here. Microscopic analyses of infected plant tissues revealed that m186 is specifically blocked at the invasive growth phase after an unaffected initial penetration stage and is unable to switch to the necrotrophic lifestyle. In addition, m186 exhibits an altered cell wall and seems to be affected in its ability to produce cell-wall-degrading enzymes. The T-DNA insertion occurs in the intergenic region between two head-to-tail genes, leading to a constitutive upregulation of their expression. Complementation experiments showed that only one of these two genes, Lmepi, fully accounts for the mutant phenotype. Bioinformatics and expression analyses along with functional studies suggested that the Lmepi gene encodes for the highly conserved UDP-glucose-4-epimerase, a key enzyme of the Leloir pathway involved in galactose metabolism. For the third time, this study highlights the intimate connection between primary metabolism and pathogenicity in L. maculans. This finding, along with similar data obtained from the related species Stagonospora nodorum, indicates the importance of in planta nutrition for the success of infection of plants by fungi belonging to class Dothideomycete.

Promoter Polymorphism of the Anion‐Exchange Protein 1 Associated with Severe Malarial Anemia and Fatality

The anion-exchange protein 1 (AE1 or band 3) is involved in the erythrocyte invasion of the malaria parasite Plasmodium falciparum, the adhesion of infected erythrocytes to endothelial cells, and the regulation of acid-base homeostasis, which is a critical factor for human survival in severe malaria. A variant of the AE1 gene promoter 512 base pairs (bp) distant from the transcription start site and 5699 bp from the translation start codon (AE1(-5699T-->C)) has been shown to be highly frequent in a population from the Ashanti region, Ghana. In a matched-pair case-control study (736 pairs), children heterozygous for the mutation (AE1(-5699CT)) had an increased risk of severe malarial anemia (odds ratio [OR], 1.45 [95% confidence interval {CI}, 1.05-2.01]; P<.03). In children who developed this complication, carriers of the mutation AE1(-5699C) had a higher fatality rate than those with the genotype AE1(-5699TT) (relative risk, 7.1 [95% CI, 1.0-52.8]). Moreover, in children with cerebral malaria, AE1(-5699C) was positively associated with a distinctive metabolic acidosis (P<.002), and results of luciferase assays showed higher transcriptional activity of the AE1(-5699C) allele. These results demonstrate that the AE1 promoter allele might influence the infection phenotype and the risk of fatal outcome in children with severe malaria. In this regard, a crucial role of the AE1 protein in malaria is emphasized.

Streamlined models of dementia care mapping

Dementia Care Mapping (DCM) is an observational tool that provides rich data about the quality of life and quality of care of persons with dementia in group care settings. The method is time-consuming and thus costly to implement in practice. This paper presents an attempt to 'streamline' DCM for the sake of simplifying it and reducing the financial resources required to implement it. Data were collected for 166 persons with dementia in three types of care settings. Seven streamlined time-sampling models were tested against the original DCM model. In general, results support the use of certain models for specific purposes. The strengths and limitations of these streamlined models are discussed and recommendations are made.

LmxPK4, a mitogen-activated protein kinase kinase homologue of Leishmania mexicana with a potential role in parasite differentiation

Members of the mitogen-activated protein (MAP) kinase cascade are important for the establishment of a Leishmania mexicana infection and are involved in flagellar length control, although the underlying molecular mechanisms remain to be elucidated. This study reports the cloning and characterization of LmxPK4, a MAP kinase kinase homologue of L. mexicana displaying putative plant-like regulatory phosphorylation sites. The recombinant protein has autophosphorylating activity and phosphorylates myelin basic protein. An LmxPK4 gene deletion mutant showed a proliferation defect after infection of macrophages and no or delayed lesion development in mice. Irrespective of the onset of lesion development parasites showed an early and homogeneous lesion development in re-infection experiments. This is indicative for a compensation of the null mutant phenotype. Additionally, this phenotype could be reverted by reintroduction of the wild-type gene into the deletion background. Mutants expressing loss-of-function or N-terminally truncated versions of LmxPK4 retained the null mutant phenotype. LmxPK4 is stage-specifically expressed in promastigotes and during differentiation to amastigotes, but is not detectable in amastigotes isolated from the mammalian host. Moreover, its in vitro kinase activity increases with temperature rise up to 40 degrees C. Our results suggest that LmxPK4 is involved in the differentiation process and affects virulence of Leishmania mexicana.

LmxMPK9, a mitogen-activated protein kinase homologue affects flagellar length in Leishmania mexicana

Components of mitogen-activated signal transduction pathways have been shown to be involved in flagellum biogenesis and maintenance. A mitogen-activated protein kinase homologue, designated LmxMPK9 from Leishmania mexicana, has been recently identified in a homology screen and its mRNA found to be present in all life stages. Three different splice-addition sites were used for mRNA maturation in trans-splicing in the different life stages. However, here we show that LmxMPK9 protein is exclusively found in the promastigote stage. Recombinant expression of LmxMPK9 in Escherichia coli and kinase assays revealed a temperature optimum at 27 degrees C, the optimal growth temperature for L. mexicana promastigotes, and a preference for manganese to promote substrate phosphorylation of myelin basic protein. A deletion mutant for the single-copy gene revealed significantly elongated flagella, whereas overexpression led to a subpopulation with rather short to no flagella suggesting a role for LmxMPK9 in flagellar morphogenesis.

Influence of cognitive impairment, functional impairment and care setting on dementia care mapping results

Quality of life (QOL) for people with dementia has become a major focus over the past decade. Dementia care mapping (DCM) is an observational measure of quality of care given by staff in formal care settings, as well as a measure of QOL that has been used in many studies of people with dementia in residential care settings. However, the method itself has not been rigorously studied in a scientific manner. For this report, mapping data were collected for 166 persons with dementia in three types of care settings: special care facilities that are licensed nursing homes, assisted living facilities, and adult day centers. The relationships between DCM and several independent variables including cognitive status, functional status, care setting, depression, length of stay, and co-morbid illnesses were assessed. Both cognitive status and functional status were found to be associated with DCM scores. Moreover, DCM was sensitive in differentiating among persons with four levels of cognitive impairment. Implications for practice are discussed.

Indications courantes de la photothérapie dynamique dans la dégénérescence maculaire liée à l’âge

Exudative age-related macular degeneration (ARMD) is now benefitting from new therapeutic approaches. Three international randomized clinical trials have demonstrated the efficacy of photodynamic therapy (PDT) in stabilizing visual acuity at 2 years. PDT is based on the activation of a photosensitizer with an adapted wavelength. In age-related macular degeneration, the photosensitizer used is verteporfin (Visudyne), which accumulates preferentially in choroidal new vessels. Functional results are obtained on the basis of a strict classification based on fluorescein angiography examining the type of the new vessels responsible for exudative ARMD. Thus, subfoveal lesions, either predominantly classic (>50%) or occult only, are the indication for PDT. Classic CNVs where laser photocoagulation thermal burns extend into the foveola may be an extrapolation of the indication for PDT. In addition, fluorescein angiography is essential for considering retreatment, usually necessary. Demonstrated growth and the persistence of leakage from the CNV is an absolute indication for a new session of PDT. A number of features still require assessment in order to define the responder group more accurately and to refine and possibly simplify the indications for retreatment.

Protein kinase involved in flagellar-length control

During its life cycle, the parasitic protozoon Leishmania mexicana differentiates from a flagellated form, the promastigote, to an amastigote form carrying a rudimentary flagellum. Besides biochemical changes, this process involves a change in overall cell morphology including flagellar shortening. A mitogen-activated protein kinase kinase homologue designated LmxMKK was identified in a homology screening and found to be critically involved in the regulation of flagellar assembly and cell size. LmxMKK is exclusively expressed in the promastigote stage and is likely to be regulated by posttranslational mechanisms such as phosphorylation. A deletion mutant for the single-copy gene revealed motile flagella dramatically reduced in length and lacking the paraflagellar rod, a structure adjacent to the axoneme in kinetoplastid flagella. Moreover, a fraction of the cells showed perturbance of the axonemal structure. Complementation of the deletion mutant with the wild-type gene restored typical promastigote morphology. We propose that LmxMKK influences anterograde intraflagellar transport to maintain flagellar length in Leishmania promastigotes; as such, it is the first protein kinase known to be involved in organellar assembly.

Mitochondrial DNA restriction map for the Caribbean fruit fly, Anastrepha suspensa, and occurrence of mitochondrial DNA diversity within highly inbred colonies

A restriction map has been constructed for Anastrepha suspensa mitochondrial DNA. One HaeIII site was found to be polymorphic among individuals in highly inbred colonies and a feral population. Based on mapping information, the polymorphic site was determined to be in the ATPase 6 gene. Primers TK-J-3804 and C3-N-5460 amplified this region. The amplicon was cut by HaeIII in flies of one haplotype and not cut in flies of the other haplotype. From 30 to 43% of the individual flies studied had this additional HaeIlI site. After cloning of the approximately 5200 bp XbaI fragment, the two mitotypes were identified. A 988 base fragment, coding for the entire tRNA-Lys(AAG), tRNA-Asp(GAC), and ATPase 8genes, and a partial ATPase 6gene was sequenced Four silent mutations, including the one at the informative site were located. The HaeIII polymorphism and other sequence differences may prove useful as a diagnostic for identification of the origin of introduced fruit flies.

[Photodynamic therapy]

Photodynamic therapy with Verteporfine (Visudyne Novartis Ophthalmics) achieves a photo occlusion of subfoveal choroidal neovascularization (CNV) resulting from age-related macular degeneration (AMD) in phase 1 and 2 studies. Thereafter, two international randomized clinical trials evaluated the product's efficacy in term of visual acuity. Eyes with neovascular lesions due to AMD of less than 5,400 micro, in size involving the fovea and presenting well-defined CNV on fluorescein angiography could be included when visual acuity was between 5 and 1/10. Six hundred and nine patients were subsequently randomized either to Verteporfine or to placebo (proportion 2:1). A follow-up of 3 months made it possible to consider retreatment when a fluorescein leakage was observed. Functional and angiographic results demonstrated the efficacy of PDT with Verteporfine in comparison with placebo at each examination during follow-up. A visual acuity decrease of less than 15 letters on ETDRS (or 3 lines or approximately 1.5/10) occured less frequently in the treated group with PDT (61% out of 402 treated eyes compared with 46% of 207 placebo eyes). Subgroup analysis of predominantly well-defined CNV (involving 50% or more of the total of the exsudative lesion) showed even more favourable effects (67% of treated eyes versus 39% of placebo eyes). Conversely, when well-defined CNV extended to a smaller area, the results were not significant. The most frequent side effect was Verteporfine extravasation at the injection site. As dynamic phototherapy with Verteporfine limits the decrease in visual acuity always occurring in the natural history of CNV caused by AMD, it is desirable that patients presenting subfoveal predominantly well-defined lesions benefit from this new treatment approach.

Shorter discharge time after regional or intravenous anaesthesia in combination with laryngeal mask airway compared with balanced anaesthesia with endotracheal intubation

BACKGROUND AND OBJECTIVE

The efficiency of operating room times can be significantly improved using rapid changes between operative procedures. We performed a retrospective analysis using electronic anaesthesia charts that compared anaesthesia-related times between the three most frequently performed types of anaesthesia (for orthopaedic surgery) to evaluate the potential for a quicker turn-around between cases.

METHODS

A total of 5614 anaesthetic procedures in trauma-related orthopaedic surgery were performed from 1997 to 1999. All were documented with an automatic record-keeping system. Data were compared for intravenous anaesthesia with the laryngeal mask airway, balanced anaesthesia with tracheal intubation and regional anaesthesia. The primary outcome measure was the time needed for emergence from anaesthesia after the end of surgery. Statistical evaluation was performed with matched triples for all three types of anaesthesia (155 triples for ambulatory surgery, 249 triples for in-patient care).

RESULTS

For ambulatory surgery, the induction time was significantly shorter for general anaesthesia (23.7 min for intravenous anaesthesia, 22.7 min for balanced anaesthesia techniques) compared with regional anaesthesia (27.2 min). The time from the end of the surgical procedure to transfer of the patient out of the operating room was shortest for regional anaesthesia (6.3 min) compared with intravenous anaesthesia (9.0 min) and balanced anaesthesia (12.5 min) techniques. Results were comparable for in-patients: regional anaesthesia required significantly longer for its induction, but less time for patient discharge from the operating room.

CONCLUSIONS

The use of a regional anaesthesia technique or one involving intravenous anaesthesia in combination with the laryngeal mask airway may lead to a reduction in discharge time compared with a balanced anaesthesia technique with endotracheal intubation. Thus, improved use of resources may be achieved.

[New therapies for the treatment of age-related macular degeneration]

Age-related macular degeneration has a natural progression from the precursors (the drusen) towards atrophic or neovascular complications. Choroidal neovascularization is undoubtedly the aspect of the disease that benefits most from new therapeutical approaches. Destructive photocoagulation based on fluorescein angiography has demonstrated since 20 years its efficiency on choroidal neovascularization. The same approach based on indocyanine green (ICG) angiography would increase the number of patients available to therapy. Very recently photodynamic therapy has demonstrated its efficiency to stabilize visual acuity at least at two years in patients with choroidal new vessels predominantly well defined. Other treatment developments are considered, such as refinement of photocoagulation techniques or of surgery. Until now, none has demonstrated its efficiency although they raise justified hopes. The future approaches rely upon the progress of the research both in physiopathology of the disease and on the angiogenic process requiring a constant interaction with all thematics of research. Finally, palliative treatments will be required before heading up to a preventive treatment.

CDKN2A/p16 inactivation is related to pituitary adenoma type and size

p16 (CDKN2A, MTS1, INK4A) status at genomic and protein levels was analysed and correlated with clinico-pathological features in 72 pituitary adenomas. Methylation of CpG islands of promoter/exon 1 sequences was found in most gonadotroph, lactotroph, plurihormonal, and null cell adenomas (36 of 44, 82%), but it was rare in somatotroph (1 of 13 cases, 8%) and corticotroph adenomas (1 of 15 cases, 7%). Homozygous CDKN2A deletion was restricted to rare somatotroph (15%) and corticotroph adenomas (13%). Immunohistochemical p16 protein expression was observed in the normal adenohypophysis, whereas it was absent in 60 of 72 (83%) tumours and reduced in another ten (14%) tumours. Staining for p16 was only seen in 5 of 15 (33%) corticotroph, 3 of 13 (23%) somatotroph, 3 of 5 (60%) plurihormonal, and 1 of 19 (5%) null cell adenomas. p16 immunonegativity without CDKN2A methylation or deletion occurred in 22 tumours, including most somatotroph and corticotroph adenomas (15 of 28, 54%). Both CDKN2A alterations and p16 negativity were related to larger tumour size. Patients with p16-negative tumours were older than patients with p16-positive tumours. These data suggest that p16 down-regulation is common in all adenoma types. The mechanisms of p16 down-regulation probably involve CDKN2A methylation in most types, but remain to be determined in somatotroph and corticotroph adenomas. These findings also suggest that p16 down-regulation is usually not an initial event, but is acquired during adenoma progression.

How do people know?

To fully understand processes of knowing and knowledge acquisition, it is necessary to examine people's understanding of their own knowing. Individual and developmental differences in what it means to know something, and hence in the criteria for justifying knowledge claims, have potentially wide-ranging implications. In providing support for a claim, young children have difficulty differentiating explanation of why a claim makes sense and evidence that the claim is true. Epistemic understanding progresses developmentally, but substantial variation remains among adults, with few adults achieving understanding of the complementary strengths and weaknesses of evidence and explanation in argument. Epistemic understanding shapes intellectual values and hence the disposition (as opposed to competence) to exercise intellectual skills. Only its most advanced levels support a disposition to engage in the intellectual effort that reasoned argument entails. The sample case of juror reasoning illustrates how epistemic understanding underlies and shapes intellectual performance.