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92 Publications

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    08/01/06 | Olfactory neuronal dynamics in behaving animals.
    Rinberg D, Gelperin A
    Seminars in Cell & Developmental Biology. 2006 Aug;17(4):454-61. doi: 10.1523/JNEUROSCI.3613-08.2008

    More than 50 years have passed since the first recording of neuronal responses to an odor stimulus from the primary olfactory brain area, the main olfactory bulb. During this time very little progress has been achieved in understanding neuronal dynamics in the olfactory bulb in awake behaving animals, which is very different from that in anesthetized preparations. In this paper we formulate a new framework containing the main reasons for studying olfactory neuronal dynamics in awake animals and review advances in the field within this new framework.

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    08/01/06 | Where to start and when to stop.
    Tian L, Matouschek A
    Nature Structural & Molecular Biology. 2006 Aug;13(8):668-70. doi: 10.1038/nsmb0806-668

    The activity of a handful of transcription factors, such as mammalian NF-B, Drosophila melanogaster Cubitus interruptus and yeast Spt23 and Mga2, are regulated through partial protein degradation by the proteasome. New data now show that the proteasome activates membrane-bound Spt23 and Mga2 by initiating their proteolysis at an internal site and then degrading the proteins bidirectionally toward both ends of the polypeptide chain, modifying our ideas on how the proteasome degrades targeted substrates.

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    07/12/06 | Toward chiral sum-frequency spectroscopy.
    Ji N, Ostroverkhov V, Belkin M, Shiu Y, Shen Y
    Journal of the American Chemical Society. 2006 Jul 12;128(27):8845-8. doi: 10.1021/ja060888c

    Chiral sum-frequency (SF) spectroscopy that measures both the real and the imaginary components of the SF spectral response was demonstrated for the first time. It was based on interference of the SF signal with a dispersionless SF reference. Solutions of 1,1’-bi-2-naphthol (BN) were used as model systems, and their chiral SF spectra over the first exciton-split transitions were obtained. Chiral spectra are useful for determination of absolute configuration and conformation of chiral molecules.

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    07/07/06 | Developmental biology. Morphing into shape.
    Stern DL
    Science. 2006 Jul 7;313(5783):50-1. doi: 10.1126/science.1130785
    07/01/06 | Identification of a glycolytic regulon in the archaea Pyrococcus and Thermococcus.
    van de Werken HJ, Verhees CH, Akerboom J, de Vos WM, van der Oost J
    FEMS Microbiology Letters. 2006 Jul;260(1):69-76. doi: 10.1111/j.1574-6968.2006.00292.x

    The glycolytic pathway of the hyperthermophilic archaea that belong to the order Thermococcales (Pyrococcus, Thermococcus and Palaeococcus) differs significantly from the canonical Embden-Meyerhof pathway in bacteria and eukarya. This archaeal glycolysis variant consists of several novel enzymes, some of which catalyze unique conversions. Moreover, the enzymes appear not to be regulated allosterically, but rather at transcriptional level. To elucidate details of the gene expression control, the transcription initiation sites of the glycolytic genes in Pyrococcus furiosus have been mapped by primer extension analysis and the obtained promoter sequences have been compared with upstream regions of non-glycolytic genes. Apart from consensus sequences for the general transcription factors (TATA-box and BRE) this analysis revealed the presence of a potential transcription factor binding site (TATCAC-N(5)-GTGATA) in glycolytic and starch utilizing promoters of P. furiosus and several thermococcal species. The absence of this inverted repeat in Pyrococcus abyssi and Pyrococcus horikoshii probably reflects that their reduced catabolic capacity does not require this regulatory system. Moreover, this phyletic pattern revealed a TrmB-like regulator (PF0124 and TK1769) which may be involved in recognizing the repeat. This Thermococcales glycolytic regulon, with more than 20 genes, is the largest regulon that has yet been described for Archaea.

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    07/01/06 | The pea aphid, Acyrthosiphon pisum: an emerging genomic model system for ecological, developmental and evolutionary studies.
    Brisson JA, Stern DL
    Bioessays. 2006 Jul;28(7):747-55. doi: 10.1002/bies.20436

    Aphids display an abundance of adaptations that are not easily studied in existing model systems. Here we review the biology of a new genomic model system, the pea aphid, Acyrthosiphon pisum. We then discuss several phenomena that are particularly accessible to study in the pea aphid: the developmental genetic basis of polyphenisms, aphid-bacterial symbioses, the genetics of adaptation and mechanisms of virus transmission. The pea aphid can be maintained in the laboratory and natural populations can be studied in the field. These properties allow controlled experiments to be performed on problems of direct relevance to natural aphid populations. Combined with new genomic approaches, the pea aphid is poised to become an important model system for understanding the molecular and developmental basis of many ecologically and evolutionarily relevant problems.

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    06/23/06 | Crystal structure of human pyrroline-5-carboxylate reductase.
    Meng Z, Lou Z, Liu Z, Li M, Zhao X, Bartlam M, Rao Z
    Journal of Molecular Biology. 2006 Jun 23;359(5):1364-77. doi: 10.1016/j.jmb.2006.04.053

    Pyrroline-5-carboxylate reductase (P5CR) is a universal housekeeping enzyme that catalyzes the reduction of Delta(1)-pyrroline-5-carboxylate (P5C) to proline using NAD(P)H as the cofactor. The enzymatic cycle between P5C and proline is very important for the regulation of amino acid metabolism, intracellular redox potential, and apoptosis. Here, we present the 2.8 Angstroms resolution structure of the P5CR apo enzyme, its 3.1 Angstroms resolution ternary complex with NAD(P)H and substrate-analog. The refined structures demonstrate a decameric architecture with five homodimer subunits and ten catalytic sites arranged around a peripheral circular groove. Mutagenesis and kinetic studies reveal the pivotal roles of the dinucleotide-binding Rossmann motif and residue Glu221 in the human enzyme. Human P5CR is thermostable and the crystals were grown at 37 degrees C. The enzyme is implicated in oxidation of the anti-tumor drug thioproline.

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    06/15/06 | Wlds protection distinguishes axon degeneration following injury from naturally occurring developmental pruning.
    Hoopfer ED, McLaughlin T, Watts RJ, Schuldiner O, O’Leary DD, Luo L
    Neuron. 2006 Jun 15;50(6):883-95. doi: 10.1016/j.neuron.2006.05.013

    Axon pruning by degeneration remodels exuberant axonal connections and is widely required for the development of proper circuitry in the nervous system from insects to mammals. Developmental axon degeneration morphologically resembles injury-induced Wallerian degeneration, suggesting similar underlying mechanisms. As previously reported for mice, we show that Wlds protein substantially delays Wallerian degeneration in flies. Surprisingly, Wlds has no effect on naturally occurring developmental axon degeneration in flies or mice, although it protects against injury-induced degeneration of the same axons at the same developmental age. By contrast, the ubiquitin-proteasome system is intrinsically required for both developmental and injury-induced axon degeneration. We also show that the glial cell surface receptor Draper is required for efficient clearance of axon fragments during developmental axon degeneration, similar to its function in injury-induced degeneration. Thus, mechanistically, naturally occurring developmental axon pruning by degeneration and injury-induced axon degeneration differ significantly in early steps, but may converge onto a common execution pathway.

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    06/13/06 | Remarkably high activities of testicular cytochrome c in destroying reactive oxygen species and in triggering apoptosis.
    Liu Z, Lin H, Ye S, Liu Q, Meng Z, Zhang C, Xia Y, Margoliash E, Rao Z, Liu X
    Proceedings of the National Academy of Sciences of the United States of America. 2006 Jun 13;103(24):8965-70. doi: 10.1073/pnas.0603327103

    Hydrogen peroxide (H(2)O(2)) is the major reactive oxygen species (ROS) produced in sperm. High concentrations of H(2)O(2) in sperm induce nuclear DNA fragmentation and lipid peroxidation and result in cell death. The respiratory chain of the mitochondrion is one of the most productive ROS generating systems in sperm, and thus the destruction of ROS in mitochondria is critical for the cell. It was recently reported that H(2)O(2) generated by the respiratory chain of the mitochondrion can be efficiently destroyed by the cytochrome c-mediated electron-leak pathway where the electron of ferrocytochrome c migrates directly to H(2)O(2) instead of to cytochrome c oxidase. In our studies, we found that mouse testis-specific cytochrome c (T-Cc) can catalyze the reduction of H(2)O(2) three times faster than its counterpart in somatic cells (S-Cc) and that the T-Cc heme has the greater resistance to being degraded by H(2)O(2). Together, these findings strongly imply that T-Cc can protect sperm from the damages caused by H(2)O(2). Moreover, the apoptotic activity of T-Cc is three to five times greater than that of S-Cc in a well established apoptosis measurement system using Xenopus egg extract. The dramatically stronger apoptotic activity of T-Cc might be important for the suicide of male germ cells, considered a physiological mechanism that regulates the number of sperm produced and eliminates those with damaged DNA. Thus, it is very likely that T-Cc has evolved to guarantee the biological integrity of sperm produced in mammalian testis.

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    06/06/06 | Cre recombinase-mediated restoration of nigrostriatal dopamine in dopamine-deficient mice reverses hypophagia and bradykinesia.
    Hnasko TS, Perez FA, Scouras AD, Stoll EA, Gale SD, Luquet S, Phillips PE, Kremer EJ, Palmiter RD
    Proceedings of the National Academy of Sciences of the United States of America. 2006 Jun 6;103(23):8858-63. doi: 10.1073/pnas.0603081103

    A line of dopamine-deficient (DD) mice was generated to allow selective restoration of normal dopamine signaling to specific brain regions. These DD floxed stop (DDfs) mice have a nonfunctional Tyrosine hydroxylase (Th) gene because of insertion of a NeoR gene flanked by lox P sites targeted to the first intron of the Th gene. DDfs mice have trace brain dopamine content, severe hypoactivity, and aphagia, and they die without intervention. However, they can be maintained by daily treatment with l-3,4-dihydroxyphenylalanine (L-dopa). Injection of a canine adenovirus (CAV-2) engineered to express Cre recombinase into the central caudate putamen restores normal Th gene expression to the midbrain dopamine neurons that project there because CAV-2 efficiently transduces axon terminals and is retrogradely transported to neuronal cell bodies. Bilateral injection of Cre recombinase into the central caudate putamen restores feeding and normalizes locomotion in DDfs mice. Analysis of feeding behavior by using lickometer cages revealed that virally rescued DDfs mice are hyperphagic and have modified meal structures compared with control mice. The virally rescued DDfs mice are also hyperactive at night, have reduced motor coordination, and are thigmotactic compared with controls. These results highlight the critical role for dopamine signaling in the dorsal striatum for most dopamine-dependent behaviors but suggest that dopamine signaling in other brain regions is important to fine-tune these behaviors. This approach offers numerous advantages compared with previous models aimed at examining dopamine signaling in discrete dopaminergic circuits.

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