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Hens K.,Institute of Bioengineering | Feuz J.-D.,Institute of Bioengineering | Isakova A.,Institute of Bioengineering | Iagovitina A.,Institute of Bioengineering | And 6 more authors.
Nature Methods

Drosophila melanogaster has one of the best characterized metazoan genomes in terms of functionally annotated regulatory elements. To explore how these elements contribute to gene regulation, we need convenient tools to identify the proteins that bind to them. Here we describe the development and validation of a high-throughput yeast one-hybrid platform, which enables screening of DNA elements versus an array of full-length, sequence-verified clones containing over 85% of predicted Drosophila transcription factors. Using six well-characterized regulatory elements, we identified 33 transcription factor-DNA interactions of which 27 were previously unidentified. To simultaneously validate these interactions and locate the binding sites of involved transcription factors, we implemented a powerful microfluidics-based approach that enabled us to retrieve DNA-occupancy data for each transcription factor throughout the respective target DNA elements. Finally, we biologically validated several interactions and identified two new regulators of sine oculis gene expression and hence eye development. © 2011 Nature America, Inc. All rights reserved. Source

Goossens T.,Laboratory of Developmental Genetics | Goossens T.,Catholic University of Leuven | Kang Y.Y.,University of Houston | Kang Y.Y.,Baylor College of Medicine | And 9 more authors.

The spatiotemporal integration of adhesion and signaling during neuritogenesis is an important prerequisite for the establishment of neuronal networks in the developing brain. In this study, we describe the role of the L1-type CAM Neuroglian protein (NRG) in different steps of Drosophila mushroom body (MB) neuron axonogenesis. Selective axon bundling in the peduncle requires both the extracellular and the intracellular domain of NRG. We uncover a novel role for the ZO-1 homolog Polychaetoid (PYD) in axon branching and in sister branch outgrowth and guidance downstream of the neuron-specific isoform NRG-180. Furthermore, genetic analyses show that the role of NRG in different aspects of MB axonal development not only involves PYD, but also TRIO, SEMA-1A and RAC1. © 2011. Published by The Company of Biologists Ltd. Source

Dermaut B.,Ghent University | Dermaut B.,Laboratory of Developmental Genetics | Seneca S.,Vrije Universiteit Brussel | Dom L.,Koningin Paola Kinderziekenhuis | And 16 more authors.
Journal of Neurology, Neurosurgery and Psychiatry

Background: m.14487T>C, a missense mutation (p.M63V) affecting the ND6 subunit of complex I of the mitochondrial respiratory chain, has been reported in isolated childhood cases with Leigh syndrome (LS) and progressive dystonia. Adult-onset phenotypes have not been reported. Objectives: To determine the clinical-neurological spectrum and associated mutation loads in an extended m.14487T>C family. Methods: A genotype-phenotype correlation study of a Belgian five-generation family with 12 affected family members segregating m.14487T>C was carried out. Clinical and mutation load data were available for nine family members. Biochemical analysis of the respiratory chain was performed in three muscle biopsies. Results: Heteroplasmic m.14487T>C levels (36-52% in leucocytes, 97-99% in muscle) were found in patients with progressive myoclonic epilepsy (PME) and dystonia or progressive hypokinetic-rigid syndrome. Patients with infantile LS were homoplasmic (99-100% in leucocytes, 100% in muscle). We found lower mutation loads (between 8 and 35% in blood) in adult patients with clinical features including migraine with aura, Leber hereditary optic neuropathy, sensorineural hearing loss and diabetes mellitus type 2. Despite homoplasmic mutation loads, complex I catalytic activity was only moderately decreased in muscle tissue. Interpretation: m.14487T>C resulted in a broad spectrum of phenotypes in our family. Depending on the mutation load, it caused severe encephalopathies ranging from infantile LS to adult-onset PME with dystonia. This is the first report of PME as an important neurological manifestation of an isolated mitochondrial complex I defect. Source

News Article | April 8, 2016
Site: http://www.biosciencetechnology.com/rss-feeds/all/rss.xml/all

Some cells are meant to live, and some are meant to die. The linker cell of Caenorhabditis elegans, a tiny worm that is a favored model organism for biologists, is among those destined for termination. This cell helps determine the shape of the gonad in male worms--and then it dies, after two days, just as the worms are transitioning from larvae into adults. This programmed cell death is a normal part of the animal's development, yet the genetic and molecular mechanisms underpinning it have not been worked out. Scientists in Rockefeller University's Laboratory of Developmental Genetics, headed by Shai Shaham, had previously shown that the linker cell does not expire by apoptosis, a more commonly studied form of programmed cell death. "Everything about this death process is different from apoptosis," he says. "It looks different under the microscope, it requires different genes, and it has different kinetics." Many ways for cells to die have been observed and described in the artificial milieu of a tissue culture dish, but not in a living organism. Now, the Shaham lab has been able to study the molecular mechanism that causes linker cell death in worms. Their findings, reported in eLife, suggest that the linker cell's newly discovered dying process resembles that which leads to the loss of neurons, or neuronal parts, in people with some neurodegenerative disorders. A new role for an old protein To figure out the molecular processes that cause linker cell death, Shaham's team introduced mutations at random in worms and then searched for animals in which the linker cell survives for longer than normal. They identified a number of mutations that prolong the survival of linker cells, including one that affects the function of HSF-1, a protein known to shield cells from physiological stresses like heat. "It was a big surprise that HSF-1, which typically plays a protective role in the cell, was found to be such a key regulator of this cell death," notes Shaham. His lab found that the protein performs two separate tasks in the cell that are independent from one another. So much so that when worms with a normal, functional HSF-1 were raised at high temperatures, their linker cells survived for longer than they normally do--presumably because the protein was kept busy protecting the cells from the heat, and hence failed to promote linker cell death. HSF-1 kills the linker cell by activating specific components of a protein destruction machinery apparatus in the cell, called the ubiquitin proteasome system. Mutations in components of this machinery have been shown previously to influence the degradation of neuron extensions in Drosophila and mice, suggesting that the new worm pathway may be used broadly. Apoptosis, one form of programmed cell suicide, is well described--scientists know which molecules induce it, which molecules suppress it, and the processes that take place in the cell as it occurs. However, blocking apoptosis in mice appears to have little effect on overall mouse development. "This is a surprising observation, given how prevalent cell death is during growth," Shaham notes. "It suggests that other means of killing cells likely exist that we know little about." Non-apoptotic cell death is also seen in some disease states. In the current study, the researchers found that the process in which linker cells are culled during a worm's development resembles the way brain neurons die during normal development in mice, and in people with Huntington's disease and other neurodegenerative disorders. It is also reminiscent of the neuronal cell death seen when nerve cells get severed, as they do during spinal injuries. Based on their recent findings in worms, Shaham and his coworkers hope to find out whether the human counterparts of the proteins promoting linker cell death in worms might be involved in neurodegeneration. If this turns out to be the case, these proteins might serve as targets for future drugs to slow the progression of Huntington's disease, or to help people regain mobility after a spinal injury. "For example, if we stress the nerve cells while they are dying, so that the HSF-1 protein is forced to go into protective mode rather than cell killing mode, perhaps we can slow their death," speculates Shaham.

Forero D.A.,Applied Genomics | Forero D.A.,University of Antwerp | Forero D.A.,Laboratory of Developmental Genetics | Forero D.A.,Catholic University of Leuven | And 7 more authors.
Human Mutation

MicroRNAs (miRNAs) are a class of nonprotein coding genes with a growing importance in regulatory mechanisms of gene expression related to brain function and plasticity. Considering the relative lack of success of the analysis of variations in candidate protein coding genes and of genome-wide association studies to identify strong risk factors for common psychiatric disorders (PDs), miRNA genes are of particular interest for the field of psychiatric genetics as deregulation of the rate of transcription or translation of a normal gene may be phenotypically similar to disruption of the gene itself. In this article we review the current knowledge on the contribution of miRNAs in basic mechanisms of brain development and plasticity and their possible involvement in the pathogenesis of several PDs. Because future functional and genomic explorations of brain expressed miRNAs, and other types of noncoding RNAs, may identify additional candidate genes and pathways for common PDs, we believe that implementing additional strategies to further elucidate the role of miRNAs in the etiology of common PDs is of great importance. Hum Mutat 31:1-10, 2010. © 2010 Wiley-Liss, Inc. Source

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