Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays

Not until recently have custom made high-density oligonucleotide microarrays been available at an affordable price. The aim of this thesis was to design microarrays and analysis algorithms for DNA repair and DNA damage detection, and to apply the methods in real experiments. Thomassen et al. have used their custom designed whole genome-tiling microarrays for detection of transcriptional changes in Escherichia coli after exposure to DNA damageing reagents. The transcriptional changes in E. coli treated with UV light or the methylating reagent MNNG were shown to be larger and to include far more genes than previously reported. To optimize the data analysis for the custom made arrays, Thomassen and coworkers designed their own normalization and analysis algorithms, and showed these more suitable than established methods that are currently applied on custom tiling arrays. Among other findings several novel stress-induced transcripts were detected, of which one is predicted to be a UV-induced short transmembrane protein. Additionally, no upregulation of the previously described UV-inducible aidB is shown. In the MNNG study several genes are shown as downregulated in response to DNA damage although having upstream regulatory sequences similar to the established LexA box A and B. This indicates that the LexA regulon also might control gene repression and that the box A and B sequence can not alone answer for the LexA controlled gene regulation. Thomassen et al. have also custom designed a microarray for oncogenic fusion gene detection. Cancer specific fusion genes are often used to subgroup cancers and to define the optimal treatment, but currently the laboratory detection procedure is both laborious and tedious. In a blinded study on six cancer cell lines proof of principle was shown by detection of six out of six positive controls. The design and analysis methods for this microarray are now being refined to make a diagnostic fusion gene detection tool

Clonal human fetal ventral mesencephalic dopaminergic neuron precursors for cell therapy research

A major challenge for further development of drug screening procedures, cell replacement therapies and developmental studies is the identification of expandable human stem cells able to generate the cell types needed. We have previously reported the generation of an immortalized polyclonal neural stem cell (NSC) line derived from the human fetal ventral mesencephalon (hVM1). This line has been biochemically, genetically, immunocytochemically and electrophysiologically characterized to document its usefulness as a model system for the generation of A9 dopaminergic neurons (DAn). Long-term in vivo transplantation studies in parkinsonian rats showed that the grafts do not mature evenly. We reasoned that diverse clones in the hVM1 line might have different abilities to differentiate. In the present study, we have analyzed 9 hVM1 clones selected on the basis of their TH generation potential and, based on the number of v-myc copies, v-myc down-regulation after in vitro differentiation, in vivo cell cycle exit, TH+ neuron generation and expression of a neuronal mature marker (hNSE), we selected two clones for further in vivo PD cell replacement studies. The conclusion is that homogeneity and clonality of characterized NSCs allow transplantation of cells with controlled properties, which should help in the design of long-term in vivo experimentsThis work was supported by grants from the Spanish Ministry of Economy and Competitiveness (formerly Science and Innovation; PLE2009-0101, SAF2010-17167), Comunidad Autónoma Madrid (S2011-BMD-2336), Instituto Salud Carlos III (RETICS TerCel, RD06/0010/0009) and European Union (Excell, NMP4-SL-2008-214706). This work was also supported by an institutional grant from Foundation Ramón Areces to the Center of Molecular Biology Severo Ocho

The Wnt Co-Receptor Lrp6 Is Required for Normal Mouse Mammary Gland Development

Canonical Wnt signals are transduced through a Frizzled receptor and either the LRP5 or LRP6 co-receptor; such signals play central roles during development and in disease. We have previously shown that Lrp5 is required for ductal stem cell activity and that loss of Lrp5 delays normal mammary development and Wnt1-induced tumorigenesis. Here we show that canonical Wnt signals through the Lrp6 co-receptor are also required for normal mouse mammary gland development. Loss of Lrp6 compromises Wnt/β-catenin signaling and interferes with mammary placode, fat pad, and branching development during embryogenesis. Heterozygosity for an inactivating mutation in Lrp6 is associated with a reduced number of terminal end buds and branches during postnatal development. While Lrp6 is expressed in both the basal and luminal mammary epithelium during embryogenesis, Lrp6 expression later becomes restricted to cells residing in the basal epithelial layer. Interestingly, these cells also express mammary stem cell markers. In humans, increased Lrp6 expression is associated with basal-like breast cancer. Taken together, our results suggest both overlapping and specific functions for Lrp5 and Lrp6 in the mammary gland

Functional Integration of Grafted Neural Stem Cell-Derived Dopaminergic Neurons Monitored by Optogenetics in an In Vitro Parkinson Model

Intrastriatal grafts of stem cell-derived dopamine (DA) neurons induce behavioral recovery in animal models of Parkinson's disease (PD), but how they functionally integrate in host neural circuitries is poorly understood. Here, Wnt5a-overexpressing neural stem cells derived from embryonic ventral mesencephalon of tyrosine hydroxylase-GFP transgenic mice were expanded as neurospheres and transplanted into organotypic cultures of wild type mouse striatum. Differentiated GFP-labeled DA neurons in the grafts exhibited mature neuronal properties, including spontaneous firing of action potentials, presence of post-synaptic currents, and functional expression of DA D2 autoreceptors. These properties resembled those recorded from identical cells in acute slices of intrastriatal grafts in the 6-hydroxy-DA-induced mouse PD model and from DA neurons in intact substantia nigra. Optogenetic activation or inhibition of grafted cells and host neurons using channelrhodopsin-2 (ChR2) and halorhodopsin (NpHR), respectively, revealed complex, bi-directional synaptic interactions between grafted cells and host neurons and extensive synaptic connectivity within the graft. Our data demonstrate for the first time using optogenetics that ectopically grafted stem cell-derived DA neurons become functionally integrated in the DA-denervated striatum. Further optogenetic dissection of the synaptic wiring between grafted and host neurons will be crucial to clarify the cellular and synaptic mechanisms underlying behavioral recovery as well as adverse effects following stem cell-based DA cell replacement strategies in PD

Altered synaptic properties during integration of adult-born hippocampal neurons following a seizure insult

Pathological conditions affect several stages of neurogenesis in the adult brain, including proliferation, survival, cell fate, migration, and functional integration. Here we explored how a pathological environment modulates the heterogeneous afferent synaptic input that shapes the functional properties of newly formed neurons. We analyzed the expression of adhesion molecules and other synaptic proteins on adult-born hippocampal neurons formed after electrically-induced partial status epilepticus (pSE). New cells were labeled with a GFP-retroviral vector one week after pSE. One and three weeks thereafter, synaptic proteins were present on dendritic spines and shafts, but without differences between pSE and control group. In contrast, at six weeks, we found fewer dendritic spines and decreased expression of the scaffolding protein PSD-95 on spines, without changes in expression of the adhesion molecules N-cadherin or neuroligin-1, primarily located at excitatory synapses. Moreover, we detected an increased expression of the inhibitory scaffolding protein gephyrin in newborn but not mature neurons after SE. However, this increase was not accompanied by a difference in GABA expression, and there was even a region-specific decrease in the adhesion molecule neuroligin-2 expression, both in newborn and mature neurons. Neuroligin-2 clusters co-localized with presynaptic cholecystokinin terminals, which were also reduced. The expression of neuroligin-4 and glycine receptor was unchanged. Increased postsynaptic clustering of gephyrin, without an accompanying increase in GABAergic input or neuroligin-2 and -4 expression, the latter important for clustering of GABAA and glycine receptors, respectively, could imply an increased but altered inhibitory connectivity specific for newborn neurons. The changes were transient and expression of both gephyrin and NL-2 was normalized 3 months post-SE. Our findings indicate that seizure-induced brain pathology alters the sub-cellular expression of synaptic adhesion molecules and scaffolding proteins related to particularly inhibitory but also excitatory synapses, which may yield functional consequences for the integration of adult-born neurons

On the freezing of variables in random constraint satisfaction problems

The set of solutions of random constraint satisfaction problems (zero energy groundstates of mean-field diluted spin glasses) undergoes several structural phase transitions as the amount of constraints is increased. This set first breaks down into a large number of well separated clusters. At the freezing transition, which is in general distinct from the clustering one, some variables (spins) take the same value in all solutions of a given cluster. In this paper we study the critical behavior around the freezing transition, which appears in the unfrozen phase as the divergence of the sizes of the rearrangements induced in response to the modification of a variable. The formalism is developed on generic constraint satisfaction problems and applied in particular to the random satisfiability of boolean formulas and to the coloring of random graphs. The computation is first performed in random tree ensembles, for which we underline a connection with percolation models and with the reconstruction problem of information theory. The validity of these results for the original random ensembles is then discussed in the framework of the cavity method.Comment: 32 pages, 7 figure

Determination of the Bending Rigidity of Graphene via Electrostatic Actuation of Buckled Membranes

The small mass and atomic-scale thickness of graphene membranes make them highly suitable for nanoelectromechanical devices such as e.g. mass sensors, high frequency resonators or memory elements. Although only atomically thick, many of the mechanical properties of graphene membranes can be described by classical continuum mechanics. An important parameter for predicting the performance and linearity of graphene nanoelectromechanical devices as well as for describing ripple formation and other properties such as electron scattering mechanisms, is the bending rigidity, {\kappa}. In spite of the importance of this parameter it has so far only been estimated indirectly for monolayer graphene from the phonon spectrum of graphite, estimated from AFM measurements or predicted from ab initio calculations or bond-order potential models. Here, we employ a new approach to the experimental determination of {\kappa} by exploiting the snap-through instability in pre-buckled graphene membranes. We demonstrate the reproducible fabrication of convex buckled graphene membranes by controlling the thermal stress during the fabrication procedure and show the abrupt switching from convex to concave geometry that occurs when electrostatic pressure is applied via an underlying gate electrode. The bending rigidity of bilayer graphene membranes under ambient conditions was determined to be $35.5^{+20}_{-15}$ eV. Monolayers have significantly lower {\kappa} than bilayers

Mutation, selection, and ancestry in branching models: a variational approach

We consider the evolution of populations under the joint action of mutation and differential reproduction, or selection. The population is modelled as a finite-type Markov branching process in continuous time, and the associated genealogical tree is viewed both in the forward and the backward direction of time. The stationary type distribution of the reversed process, the so-called ancestral distribution, turns out as a key for the study of mutation-selection balance. This balance can be expressed in the form of a variational principle that quantifies the respective roles of reproduction and mutation for any possible type distribution. It shows that the mean growth rate of the population results from a competition for a maximal long-term growth rate, as given by the difference between the current mean reproduction rate, and an asymptotic decay rate related to the mutation process; this tradeoff is won by the ancestral distribution. Our main application is the quasispecies model of sequence evolution with mutation coupled to reproduction but independent across sites, and a fitness function that is invariant under permutation of sites. Here, the variational principle is worked out in detail and yields a simple, explicit result.Comment: 45 pages,8 figure

Reprogramming the diseased brain

Direct conversion of astrocytes to dopamine neurons in vivo offers fresh optimism for the development of improved Parkinson's therapie

Targeted Delivery of Neural Stem Cells to the Brain Using MRI-Guided Focused Ultrasound to Disrupt the Blood-Brain Barrier

Stem cell therapy is a promising strategy to treat neurodegenerative diseases, traumatic brain injury, and stroke. For stem cells to progress towards clinical use, the risks associated with invasive intracranial surgery used to deliver the cells to the brain, needs to be reduced. Here, we show that MRI-guided focused ultrasound (MRIgFUS) is a novel method for non-invasive delivery of stem cells from the blood to the brain by opening the blood brain barrier (BBB) in specific brain regions. We used MRI guidance to target the ultrasound beam thereby delivering the iron-labeled, green fluorescent protein (GFP)-expressing neural stem cells specifically to the striatum and the hippocampus of the rat brain. Detection of cellular iron using MRI established that the cells crossed the BBB to enter the brain. After sacrifice, 24 hours later, immunohistochemical analysis confirmed the presence of GFP-positive cells in the targeted brain regions. We determined that the neural stem cells expressed common stem cell markers (nestin and polysialic acid) suggesting they survived after transplantation with MRIgFUS. Furthermore, delivered stem cells expressed doublecortin in vivo indicating the stem cells were capable of differentiating into neurons. Together, we demonstrate that transient opening of the BBB with MRIgFUS is sufficient for transplantation of stem cells from the blood to targeted brain structures. These results suggest that MRIgFUS may be an effective alternative to invasive intracranial surgery for stem cell transplantation