SPECIES DELIMITATION,TAXONOMY, AND BIOGEOGRAPHY OF DICTYOTA IN EUROPE (DICTYOTALES,PHAEOPHYCEAE)1

Taxonomy of the brown algal genus Dictyota has a long and troubled history. Our inability to distinguish morphological plasticity from fixed diagnostic traits that separate the various species has severely confounded species delineation. From continental Europe, more than 60 species and intraspecific taxa have been described over the last two centuries. Using a molecular approach, we addressed the diversity of the genus in European waters and made necessary taxonomic changes. A densely sampled DNA data set demonstrated the presence of six evolutionarily significant units (ESUs): Dictyota dichotoma (Huds.) J. V. Lamour., D. fasciola (Roth) J. V. Lamour., D. implexa J. V. Lamour., D. mediterranea (Schiffn.) G. Furnari, D. spiralis Mont., and the newly described D. cyanoloma sp. nov., which was previously reported as D. ciliolata from the Mediterranean Sea. Species distributions, based on DNA‐confirmed occurrence records, indicate that all species are geographically confined to the NE Atlantic Ocean with the exception of D. dichotoma and D. implexa, which also occur in South Africa and Bermuda, respectively. To investigate potential hybridization between D. dichotoma and D. implexa, which were previously shown to be sexually compatible in culture, we compiled and analyzed sets of mitochondrial, plastid, and nuclear markers to detect putative hybrids or introgression in natural populations. Failure to detect natural hybrids indicates that effective pre‐ and postzygotic isolation mechanisms are at play in natural populations and supports the by‐product hypothesis of reproductive isolation.     

Neuroligin 2 is exclusively localized to inhibitory synapses

Neuroligins are cell adhesion proteins that are thought to instruct the formation and alignment of synaptic specializations. The three known rodent neuroligin isoforms share homologous extracellular acetylcholinesterase-like domains that bridge the synaptic cleft and bind beta-neurexins. All neuroligins have identical intracellular C-terminal motifs that bind to PDZ domains of various target proteins. Neuroligin 1 is specifically localized to glutamatergic postsynaptic specializations. We show here that neuroligin 2 is exclusively localized to inhibitory synapses in rat brain and dissociated neurons. In immature neurons, neuroligin 2 is found at synapses and also at GABAA receptor aggregates that are not facing presynaptic termini, indicating that postsynaptic mechanisms lead to synaptic recruitment of neuroligin 2. Our findings identify neuroligin 2 as a new cell adhesion protein specific for inhibitory synapses and open new avenues for identifiying the constituents of this unique type of postsynaptic specialization.     

Chronic treatment with the gamma-secretase inhibitor LY-411,575 inhibits beta-amyloid peptide production and alters lymphopoiesis and intestinal cell differentiation

Inhibition of gamma-secretase, one of the enzymes responsible for the cleavage of the amyloid precursor protein (APP) to produce the pathogenic beta-amyloid (Abeta) peptides, is an attractive approach to the treatment of Alzheimer disease. In addition to APP, however, several other gamma-secretase substrates have been identified (e.g. Notch), and altered processing of these substrates by gamma-secretase inhibitors could lead to unintended biological consequences. To study the in vivo consequences of gamma-secretase inhibition, the gamma-secretase inhibitor LY-411,575 was administered to C57BL/6 and TgCRND8 APP transgenic mice for 15 days. Although most tissues were unaffected, doses of LY-411,575 that inhibited Abeta production had marked effects on lymphocyte development and on the intestine. LY-411,575 decreased overall thymic cellularity and impaired intrathymic differentiation at the CD4(-)CD8(-)CD44(+)CD25(+) precursor stage. No effects on peripheral T cell populations were noted following LY-411,575 treatment, but evidence for the altered maturation of peripheral B cells was observed. In the intestine, LY-411,575 treatment increased goblet cell number and drastically altered tissue morphology. These effects of LY-411,575 were not seen in mice that were administered LY-D, a diastereoisomer of LY-411,575, which is a very weak gamma-secretase inhibitor. These studies show that inhibition of gamma-secretase has the expected benefit of reducing Abeta in a murine model of Alzheimer disease but has potentially undesirable biological effects as well, most likely because of the inhibition of Notch processing.     

Efficient in vitro myogenic reprogramming of human primary mesenchymal stem cells and endothelial cells by Myf5

Background information. The identification of a source of stem cells able to regenerate skeletal muscle was the goal of numerous studies with the aim to develop new therapeutic approaches for genetic muscle diseases or muscle injuries. A series of studies have demonstrated that stem cells derived from various tissues may have a role in the regeneration of damaged muscles, but this contribution is always very weak. Thus we established a project aiming to reprogramme non‐muscle cells into the skeletal striated differentiation pathway. Results. We transduced several human primary adult stem or progenitor cells using a recombinant lentivirus containing the coding sequence of the Myf5 gene considered as a master gene for the determination of skeletal striated muscle. These original results are the first demonstration of a myogenic conversion of human mesenchymal and endothelial cells by Myf5. Conclusions. The procedure described in the present paper could be used to develop new research protocols with the prospect of using these cells as therapeutic agents.     

Getting a grip on proteomics data – Proteomics Data Collection (ProDaC)

In proteomics, rapid developments in instrumentation led to the acquisition of increasingly large data sets. Correspondingly, ProDaC was founded in 2006 as a Coordination Action project within the 6th European Union Framework Programme to support data sharing and community‐wide data collection. The objectives of ProDaC were the development of documentation and storage standards, setup of a standardized data submission pipeline and collection of data. Ending in March 2009, ProDaC has delivered a comprehensive toolbox of standards and computer programs to achieve these goals.     

Individuals with Autism Spectrum Disorders Do Not Use Social Stereotypes in Irony Comprehension

Social and communication impairments are part of the essential diagnostic criteria used to define Autism Spectrum Disorders (ASDs). Difficulties in appreciating non-literal speech, such as irony in ASDs have been explained as due to impairments in social understanding and in recognizing the speaker’s communicative intention. It has been shown that social-interactional factors, such as a listener’s beliefs about the speaker’s attitudinal propensities (e.g., a tendency to use sarcasm, to be mocking, less sincere and more prone to criticism), as conveyed by an occupational stereotype, do influence a listener’s interpretation of potentially ironic remarks. We investigate the effect of occupational stereotype on irony detection in adults with High Functioning Autism or Asperger Syndrome (HFA/AS) and a comparison group of typically developed adults. We used a series of verbally presented stories containing ironic or literal utterances produced by a speaker having either a “sarcastic” or a “non-sarcastic” occupation. Although individuals with HFA/AS were able to recognize ironic intent and occupational stereotypes when the latter are made salient, stereotype information enhanced irony detection and modulated its social meaning (i.e., mockery and politeness) only in comparison participants. We concluded that when stereotype knowledge is not made salient, it does not automatically affect pragmatic communicative processes in individuals with HFA/AS.     

Elevated Alpha-Synuclein Impairs Innate Immune Cell Function and Provides a Potential Peripheral Biomarker for Parkinson's Disease

Alpha-synuclein protein is strongly implicated in the pathogenesis Parkinson''s disease. Increased expression of α-synuclein due to genetic multiplication or point mutations leads to early onset disease. While α-synuclein is known to modulate membrane vesicle dynamics, it is not clear if this activity is involved in the pathogenic process or if measurable physiological effects of α-synuclein over-expression or mutation exist in vivo. Macrophages and microglia isolated from BAC α-synuclein transgenic mice, which overexpress α-synuclein under regulation of its own promoter, express α-synuclein and exhibit impaired cytokine release and phagocytosis. These processes were affected in vivo as well, both in peritoneal macrophages and microglia in the CNS. Extending these findings to humans, we found similar results with monocytes and fibroblasts isolated from idiopathic or familial Parkinson''s disease patients compared to age-matched controls. In summary, this paper provides 1) a new animal model to measure α-synuclein dysfunction; 2) a cellular system to measure synchronized mobilization of α-synuclein and its functional interactions; 3) observations regarding a potential role for innate immune cell function in the development and progression of Parkinson''s disease and other human synucleinopathies; 4) putative peripheral biomarkers to study and track these processes in human subjects. While altered neuronal function is a primary issue in PD, the widespread consequence of abnormal α-synuclein expression in other cell types, including immune cells, could play an important role in the neurodegenerative progression of PD and other synucleinopathies. Moreover, increased α-synuclein and altered phagocytosis may provide a useful biomarker for human PD.     

Characterization of a MAPK scaffolding protein logic gate in gonadotropes

In the pituitary gonadotropes, both protein kinase C (PKC) and MAPK/ERK signaling cascades are activated by GnRH. Phosphoprotein-enriched in astrocytes 15 (PEA-15) is a cytosolic ERK scaffolding protein, which is expressed in LβT2 gonadotrope cells. Pharmacological inhibition of PKC and small interfering RNA-mediated silencing of Gαq/11 revealed that GnRH induces accumulation of phosphorylated PEA-15 in a PKC-dependent manner. To investigate the potential role of PEA-15 in GnRH signaling, we examined the regulation of ERK subcellular localization and the activation of ribosomal S6 kinase, a substrate of ERK. Results obtained by cellular fractionation/Western blot analysis and immunohistochemistry revealed that GnRH-induced accumulation of phosphorylated ERK in the nucleus was attenuated when PEA-15 expression was reduced. Conversely, in the absence of GnRH stimulation, PEA-15 anchors ERK in the cytosol. Our data suggest that GnRH-induced nuclear translocation of ERK requires its release from PEA-15, which occurs upon PEA-15 phosphorylation by PKC. Additional gene-silencing experiments in GnRH-stimulated cells demonstrated that ribosomal S6 kinase activation was dependent on both PEA-15 and PKC. Furthermore, small interfering RNA-mediated knockdown of PEA-15 caused a reduction in GnRH-stimulated expression of early response genes Egr2 and c-Jun, as well as gonadotropin FSHβ-subunit gene expression. PEA-15 knockdown increased LHβ and common α-glycoprotein subunit mRNAs, suggesting a possible role in differential regulation of gonadotropin subunit gene expression. We propose that PEA-15 represents a novel point of convergence of the PKC and MAPK/ERK pathways under GnRH stimulation. PKC, ERK, and PEA-15 form an AND logic gate that shapes the response of the gonadotrope cell to GnRH.     

QuickMod: A tool for open modification spectrum library searches

MS2 library spectra are rich in reproducible information about peptide fragmentation patterns compared to theoretical spectra modeled by a sequence search tool. So far, spectrum library searches are mostly applied to detect peptides as they are present in the library. However, they also allow finding modified variants of the library peptides if the search is done with a large precursor mass window and an adapted Spectrum-Spectrum Match (SSM) scoring algorithm. We perform a thorough evaluation on the use of library spectra as opposed to theoretical peptide spectra for the identification of PTMs, analyzing spectra of a well-annotated modification-rich test data set compiled from public data repositories. These initial studies motivate the development of our modification tolerant spectrum library search tool QuickMod, designed to identify modified variants of the peptides listed in the spectrum library without any prior input from the user estimating the modifications present in the sample. We built the search algorithm of QuickMod after carefully testing different SSM similarity scores. The final spectrum scoring scheme uses a support vector machine (SVM) on a selection of scoring features to classify correct and incorrect SSM. After identification of a list of modified peptides at a given False Discovery Rate (FDR), the modifications need to be positioned on the peptide sequence. We present a rapid modification site assignment algorithm and evaluate its positioning accuracy. Finally, we demonstrate that QuickMod performs favorably in terms of speed and identification rate when compared to other software solutions for PTM analysis.