TY - JOUR AB - In Gram-negative bacteria, the uptake and export of a wide range of molecules, including antibiotics, is facilitated by porins and efflux pumps. Because of their role in regulating small molecule permeability of the outer and inner membrane, these transport machineries are tightly regulated at the transcriptional and post-transcriptional levels. However, regulation of transport by external chemical cues remains poorly understood. Here we investigated transcriptional regulation of three prominent transporter genes in Escherichia coli across 94 defined chemical cues, and simultaneously mapped the contributions of the key regulators MarA, SoxS and Rob to promoter activity. One third of all tested compounds triggered transcriptional changes, the majority of which were previously unknown. Importantly, we exposed main drivers of transport control in E. coli, e.g., bacteriostatic but not bactericidal antibiotics trigger the expression of efflux pumps, and Rob contributes to ~1/3 of all measured transcriptional changes, thereby emerging as a more prominent regulator of transport than previously thought. We showcase the potential of our resource by elucidating the molecular mechanism of antibiotic antagonisms with widely consumed caffeine in E. coli. Altogether, our analysis provides a quantitative overview of how different regulators orchestrate the transcriptional response of major transport determinants to environmental chemical cues. AU - Binsfeld, C.* AU - Olayo-Alarcon, R. AU - Pérez Jiménez, L.* AU - Wartel, M.* AU - Stadler, M. AU - Mateus, A.* AU - Müller, C.L. AU - Brochado, A.R.* C1 - 75224 C2 - 57852 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli. JO - PLoS Biol. VL - 23 IS - 7 PB - Public Library Science PY - 2025 SN - 1544-9173 ER - TY - JOUR AB - According to the synaptic homeostasis hypothesis (SHY), sleep serves to renormalize synaptic connections that have been potentiated during the prior wake phase due to ongoing encoding of information. SHY focuses on glutamatergic synaptic strength and has been supported by numerous studies examining synaptic structure and function in neocortical and hippocampal networks. However, it is unknown whether synaptic down-regulation during sleep occurs in the hypothalamus, i.e., a pivotal center of homeostatic regulation of bodily functions including sleep itself. We show that sleep, in parallel with the synaptic down-regulation in neocortical networks, down-regulates the levels of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) in the hypothalamus of rats. Most robust decreases after sleep were observed at both sites for AMPARs containing the GluA1 subunit. Comparing the effects of selective rapid eye movement (REM) sleep and total sleep deprivation, we moreover provide experimental evidence that slow-wave sleep (SWS) is the driving force of the down-regulation of AMPARs in hypothalamus and neocortex, with no additional contributions of REM sleep or the circadian rhythm. SWS-dependent synaptic down-regulation was not linked to EEG slow-wave activity. However, spindle density during SWS predicted relatively increased GluA1 subunit levels in hypothalamic synapses, which is consistent with the role of spindles in the consolidation of memory. Our findings identify SWS as the main driver of the renormalization of synaptic strength during sleep and suggest that SWS-dependent synaptic renormalization is also implicated in homeostatic control processes in the hypothalamus. AU - Liu, J.* AU - Niethard, N.* AU - Lun, Y.* AU - Dimitrov, S.* AU - Ehrlich, I.* AU - Born, J. AU - Hallschmid, M. C1 - 71500 C2 - 56217 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - Slow-wave sleep drives sleep-dependent renormalization of synaptic AMPA receptor levels in the hypothalamus. JO - PLoS Biol. VL - 22 IS - 8 PB - Public Library Science PY - 2024 SN - 1544-9173 ER - TY - JOUR AB - The information contained in population genomic data can tell us much about the past ecology and evolution of species. We leveraged detailed phenotypic and genomic data of nearly all living kākāpō to understand the evolution of its feather color polymorphism. The kākāpō is an endangered and culturally significant parrot endemic to Aotearoa New Zealand, and the green and olive feather colorations are present at similar frequencies in the population. The presence of such a neatly balanced color polymorphism is remarkable because the entire population currently numbers less than 250 birds, which means it has been exposed to severe genetic drift. We dissected the color phenotype, demonstrating that the two colors differ in their light reflectance patterns due to differential feather structure. We used quantitative genomics methods to identify two genetic variants whose epistatic interaction can fully explain the species' color phenotype. Our genomic forward simulations show that balancing selection might have been pivotal to establish the polymorphism in the ancestrally large population, and to maintain it during population declines that involved a severe bottleneck. We hypothesize that an extinct apex predator was the likely agent of balancing selection, making the color polymorphism in the kākāpō a "ghost of selection past." AU - Urban, L. AU - Santure, A.W.* AU - Uddstrom, L.R.* AU - Digby, A.* AU - Vercoe, D.* AU - Eason, D.* AU - Crane, J.* AU - Wylie, M.J.* AU - Davis, T.* AU - LeLec, M.F.* AU - Guhlin, J.* AU - Poulton, S.* AU - Slate, J.* AU - Alexander, A.* AU - Fuentes-Cross, P.* AU - Dearden, P.K.* AU - Gemmell, N.J.* AU - Azeem, F.* AU - Weyland, M.* AU - Schwefel, H.G.L.* AU - van Oosterhout, C.* AU - Morales, H.E.* C1 - 71656 C2 - 56334 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator. JO - PLoS Biol. VL - 22 IS - 9 PB - Public Library Science PY - 2024 SN - 1544-9173 ER - TY - JOUR AB - Over the past 20 years, 3 highly pathogenic human coronaviruses (HCoVs) have emerged-Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and, most recently, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)-demonstrating that coronaviruses (CoVs) pose a serious threat to human health and highlighting the importance of developing effective therapies against them. Similar to other viruses, CoVs are dependent on host factors for their survival and replication. We hypothesized that evolutionarily distinct CoVs may exploit similar host factors and pathways to support their replication cycles. Herein, we conducted 2 independent genome-wide CRISPR/Cas-9 knockout (KO) screens to identify MERS-CoV and HCoV-229E host dependency factors (HDFs) required for HCoV replication in the human Huh7 cell line. Top scoring genes were further validated and assessed in the context of MERS-CoV and HCoV-229E infection as well as SARS-CoV and SARS-CoV-2 infection. Strikingly, we found that several autophagy-related genes, including TMEM41B, MINAR1, and the immunophilin FKBP8, were common host factors required for pan-CoV replication. Importantly, inhibition of the immunophilin protein family with the compounds cyclosporine A, and the nonimmunosuppressive derivative alisporivir, resulted in dose-dependent inhibition of CoV replication in primary human nasal epithelial cell cultures, which recapitulate the natural site of virus replication. Overall, we identified host factors that are crucial for CoV replication and demonstrated that these factors constitute potential targets for therapeutic intervention by clinically approved drugs. AU - Kratzel, A.* AU - Kelly, J.N.* AU - V'kovski, P.* AU - Portmann, J.* AU - Brüggemann, Y.* AU - Todt, D.* AU - Ebert, N.* AU - Shrestha, N.* AU - Plattet, P.* AU - Staab-Weijnitz, C.A. AU - von Brunn, A. * AU - Steinmann, E.* AU - Dijkman, R.* AU - Zimmer, G.* AU - Pfaender, S.* AU - Thiel, V.* C1 - 63863 C2 - 51654 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - A genome-wide CRISPR screen identifies interactors of the autophagy pathway as conserved coronavirus targets. JO - PLoS Biol. VL - 19 IS - 12 PB - Public Library Science PY - 2021 SN - 1544-9173 ER - TY - JOUR AU - Lupperger, V. AU - Marr, C. AU - Chapouton, P. C1 - 61531 C2 - 50200 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - Correction: Reoccuring neural stem cell divisions in the adult zebrafish telencephalon are sufficient for the emergence of aggregated spatio-temporal patterns. JO - PLoS Biol. VL - 19 IS - 2 PB - Public Library Science PY - 2021 SN - 1544-9173 ER - TY - JOUR AB - Evo:lvPinlegaisnecsoynnfcirwmitthhatthalelhceoamdipnugtleavtieolnsarreevreopluretisoenntoevdecor rtrheectplya:st 30 years, computational biology has emerged as a mature scientific field. While the field has made major contributions toward improving scientific knowledge and human health, individual computational biology practitioners at various institutions often languish in career development. As optimistic biologists passionate about the future of our field, we propose solutions for both eager and reluctant individual scientists, institutions, publishers, funding agencies, and educators to fully embrace computational biology. We believe that in order to pave the way for the next generation of discoveries, we need to improve recognition for computational biologists and better align pathways of career success with pathways of scientific progress. With 10 outlined steps, we call on all adjacent fields to move away from the traditional individual, single-discipline investigator research model and embrace multidisciplinary, data-driven, team science. AU - Way, G.P.* AU - Greene, C.S.* AU - Carninci, P.* AU - Carvalho, B.S.* AU - de Hoon, M.* AU - Finley, S.* AU - Gosline, S.J.C.* AU - Le Cao, K.A.* AU - Lee, J.S.H.* AU - Marchionni, L.* AU - Robine, N.* AU - Sindi, S.S.* AU - Theis, F.J. AU - Yang, J.Y.H.* AU - Carpenter, A.E.* AU - Fertig, E.J.* C1 - 63257 C2 - 51411 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - A field guide to cultivating computational biology. JO - PLoS Biol. VL - 19 IS - 10 PB - Public Library Science PY - 2021 SN - 1544-9173 ER - TY - JOUR AB - Regulation of quiescence and cell cycle entry is pivotal for the maintenance of stem cell populations. Regulatory mechanisms, however, are poorly understood. In particular, it is unclear how the activity of single stem cells is coordinated within the population or if cells divide in a purely random fashion. We addressed this issue by analyzing division events in an adult neural stem cell (NSC) population of the zebrafish telencephalon. Spatial statistics and mathematical modeling of over 80,000 NSCs in 36 brain hemispheres revealed weakly aggregated, nonrandom division patterns in space and time. Analyzing divisions at 2 time points allowed us to infer cell cycle and S-phase lengths computationally. Interestingly, we observed rapid cell cycle reentries in roughly 15% of newly born NSCs. In agent-based simulations of NSC populations, this redividing activity sufficed to induce aggregated spatiotemporal division patterns that matched the ones observed experimentally. In contrast, omitting redivisions leads to a random spatiotemporal distribution of dividing cells. Spatiotemporal aggregation of dividing stem cells can thus emerge solely from the cell's history. AU - Lupperger, V. AU - Marr, C. AU - Chapouton, P. C1 - 60773 C2 - 49528 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - Reoccurring neural stem cell divisions in the adult zebrafish telencephalon are sufficient for the emergence of aggregated spatiotemporal patterns. JO - PLoS Biol. VL - 18 IS - 12 PB - Public Library Science PY - 2020 SN - 1544-9173 ER - TY - JOUR AB - Accurate genome duplication underlies genetic homeostasis. Metazoan Mdm2 binding protein (MTBP) forms a main regulatory platform for origin, firing together with Topoisomerase II binding protein 1 (TopBP1)-interacting replication stimulating protein/TopBP1-interacting checkpoint and replication regulator (Treslin/TICRR) and TopBP1. We report the first comprehensive analysis of MTBP and reveal conserved and metazoa-specific MTBP functions in replication. This suggests that metazoa have evolved specific molecular mechanisms to adapt replication principles conserved with yeast to the specific requirements of the more complex metazoan cells. We uncover one such metazoa-specific process: a new replication factor, cyclin-dependent kinase 8/19-cyclinC (Cdk8/19-cyclin C), binds to a central domain of MTBP. This interaction is required for complete genome duplication in human cells. In the absence of MTBP binding to Cdk8/19-cyclin C, cells enter mitosis with incompletely duplicated chromosomes, and subsequent chromosome segregation occurs inaccurately. Using remote homology searches, we identified MTBP as the metazoan orthologue of yeast synthetic lethal with Dpb11 7 (Sld7). This homology finally demonstrates that the set of yeast core factors sufficient for replication initiation in vitro is conserved in metazoa. MTBP and Sld7 contain two homologous domains that are present in no other protein, one each in the N and C termini. In MTBP the conserved termini flank the metazoa-specific Cdk8/19-cyclin C binding region and are required for normal origin firing in human cells. The N termini of MTBP and Sld7 share an essential origin firing function, the interaction with Treslin/TICRR or its yeast orthologue Sld3, respectively. The C termini may function as homodimerisation domains. Our characterisation of broadly conserved and metazoa-specific initiation processes sets the basis for further mechanistic dissection of replication initiation in vertebrates. It is a first step in understanding the distinctions of origin firing in higher eukaryotes. AU - Köhler, K.* AU - Sanchez-Pulido, L.* AU - Höfer, V.* AU - Marko, A.* AU - Ponting, C.P.* AU - Snijders, A.P.* AU - Feederle, R. AU - Schepers, A. AU - Boos, D.* C1 - 55355 C2 - 46337 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - The Cdk8/19-cyclin C transcription regulator functions in genome replication through metazoan Sld7. JO - PLoS Biol. VL - 17 IS - 1 PB - Public Library Science PY - 2019 SN - 1544-9173 ER - TY - JOUR AB - Animal welfare requires the adequate housing of animals to ensure health and well-being. The application of environmental enrichment is a way to improve the well-being of laboratory animals. However, it is important to know whether these enrichment items can be incorporated in experimental mouse husbandry without creating a divide between past and future experimental results. Previous small-scale studies have been inconsistent throughout the literature, and it is not yet completely understood whether and how enrichment might endanger comparability of results of scientific experiments. Here, we measured the effect on means and variability of 164 physiological parameters in 3 conditions: with nesting material with or without a shelter, comparing these 2 conditions to a “barren” regime without any enrichments. We studied a total of 360 mice from each of 2 mouse strains (C57BL/6NTac and DBA/2NCrl) and both sexes for each of the 3 conditions. Our study indicates that enrichment affects the mean values of some of the 164 parameters with no consistent effects on variability. However, the influence of enrichment appears negligible compared to the effects of other influencing factors. Therefore, nesting material and shelters may be used to improve animal welfare without impairment of experimental outcome or loss of comparability to previous data collected under barren housing conditions. AU - André, V. AU - Gau, C. AU - Scheideler, A. AU - Aguilar-Pimentel, J.A. AU - Amarie, O.V. AU - Becker, L. AU - Garrett, L. AU - Hans, W. AU - Hölter, S.M. AU - Janik, D. AU - Moreth, K. AU - Neff, F. AU - Östereicher, M.A. AU - Rácz, I. AU - Rathkolb, B. AU - Rozman, J. AU - Bekeredjian, R.* AU - Graw, J. AU - Klingenspor, M.* AU - Klopstock, T.* AU - Ollert, M.* AU - Schmidt-Weber, C.B. AU - Wolf, E.* AU - Wurst, W. AU - Gailus-Durner, V. AU - Brielmeier, M. AU - Fuchs, H. AU - Hrabě de Angelis, M. C1 - 53408 C2 - 44554 TI - Laboratory mouse housing conditions can be improved using common environmental enrichment without compromising data. JO - PLoS Biol. VL - 16 IS - 4 PY - 2018 SN - 1544-9173 ER - TY - JOUR AB - In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, but a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under different physiological conditions. At a constant external temperature of 38 °C, mitochondria were more than 10 °C warmer when the respiratory chain (RC) was fully functional, both in human embryonic kidney (HEK) 293 cells and primary skin fibroblasts. This differential was abolished in cells depleted of mitochondrial DNA or treated with respiratory inhibitors but preserved or enhanced by expressing thermogenic enzymes, such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at or slightly above 50 °C. In view of their potential consequences, these observations need to be further validated and explored by independent methods. Our study prompts a critical re-examination of the literature on mitochondria. AU - Chrétien, D.* AU - Bénit, P.* AU - Ha, H.H.* AU - Keipert, S. AU - El-Khoury, R.* AU - Chang, Y.T.* AU - Jastroch, M. AU - Jacobs, H.T.* AU - Rustin, P.* AU - Rak, M.* C1 - 52802 C2 - 44450 CY - San Francisco TI - Mitochondria are physiologically maintained at close to 50 °C. JO - PLoS Biol. VL - 16 IS - 1 PB - Public Library Science PY - 2018 SN - 1544-9173 ER - TY - JOUR AB - Circadian clocks are fundamental physiological regulators of energy homeostasis, but direct transcriptional targets of the muscle clock machinery are unknown. To understand how the muscle clock directs rhythmic metabolism, we determined genome-wide binding of the master clock regulators brain and muscle ARNT-like protein 1 (BMAL1) and REV-ERB alpha in murine muscles. Integrating occupancy with 24-hr gene expression and metabolomics after muscle-specific loss of BMAL1 and REV-ERB alpha, here we unravel novel molecular mechanisms connecting muscle clock function to daily cycles of lipid and protein metabolism. Validating BMAL1 and REV-ERB alpha targets using luciferase assays and in vivo rescue, we demonstrate how a major role of the muscle clock is to promote diurnal cycles of neutral lipid storage while coordinately inhibiting lipid and protein catabolism prior to awakening. This occurs by BMAL1-dependent activation of Dgat2 and REV-ERB alpha-dependent repression of major targets involved in lipid metabolism and protein turnover (MuRF-1, Atrogin-1). Accordingly, muscle- specific loss of BMAL1 is associated with metabolic inefficiency, impaired muscle triglyceride biosynthesis, and accumulation of bioactive lipids and amino acids. Taken together, our data provide a comprehensive overview of how genomic binding of BMAL1 and REV-ERB alpha is related to temporal changes in gene expression and metabolite fluctuations. AU - Dyar, K.A. AU - Huber, M.J. AU - Mir, A.A. AU - Ciciliot, S.* AU - Lutter, D. AU - Greulich, F. AU - Quagliarini, F. AU - Kleinert, M. AU - Fischer, K. AU - Eichmann, T.O.* AU - Wright, L.E.* AU - Peña Paz, M.I.* AU - Casarin, A.* AU - Pertegato, V.* AU - Romanello, V.* AU - Albiero, M.* AU - Mazzucco, S.* AU - Rizzuto, R.* AU - Salviati, L.* AU - Biolo, G.* AU - Blaauw, B.* AU - Schiaffino, S.* AU - Uhlenhaut, N.H. C1 - 54118 C2 - 45296 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - Transcriptional programming of lipid and amino acid metabolism by the skeletal muscle circadian clock. JO - PLoS Biol. VL - 16 IS - 8 PB - Public Library Science PY - 2018 SN - 1544-9173 ER - TY - JOUR AB - Cilia are organelles specialized in movement and signal transduction. The ciliary transient receptor potential ion channel polycystin-2 (TRPP2) controls elementary cilia-mediated physiological functions ranging from male fertility and kidney development to left–right patterning. However, the molecular components translating TRPP2 channel–mediated Ca2+signals into respective physiological functions are unknown. Here, we show that the Ca2+-regulated mitochondrial ATP-Mg/Pisolute carrier 25 A 25 (SLC25A25) acts downstream of TRPP2 in an evolutionarily conserved metabolic signaling pathway. We identify SLC25A25 as an essential component in this cilia-dependent pathway using a genome-wide forward genetic screen in Drosophila melanogaster, followed by a targeted analysis of SLC25A25 function in zebrafish left–right patterning. Our data suggest that TRPP2 ion channels regulate mitochondrial SLC25A25 transporters via Ca2+establishing an evolutionarily conserved molecular link between ciliary signaling and mitochondrial metabolism. AU - Hofherr, A.* AU - Seger, C.* AU - Fitzpatrick, F.* AU - Busch, T.* AU - Michel, E.* AU - Luan, J.* AU - Osterried, L.* AU - Linden, F.* AU - Kramer-Zucker, A.* AU - Wakimoto, B.* AU - Schütze, C.* AU - Wiedemann, N.* AU - Artati, A. AU - Adamski, J. AU - Walz, G.* AU - Kunji, E.R.S.* AU - Montell, C.* AU - Watnick, T.* AU - Köttgen, M.* C1 - 54092 C2 - 45264 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - The mitochondrial transporter SLC25A25 links ciliary TRPP2 signaling and cellular metabolism. JO - PLoS Biol. VL - 16 IS - 8 PB - Public Library Science PY - 2018 SN - 1544-9173 ER - TY - JOUR AB - While Notch signaling has been proposed to play a key role in fibrosis, the direct molecular pathways targeted by Notch signaling and the precise ligand and receptor pair that are responsible for kidney disease remain poorly defined. In this study, we found that JAG1 and NOTCH2 showed the strongest correlation with the degree of interstitial fibrosis in a genome-wide expression analysis of a large cohort of human kidney samples. Transcript analysis of mouse kidney disease models, including folic-acid (FA)–induced nephropathy, unilateral ureteral obstruction (UUO), or apolipoprotein L1 (APOL1)-associated kidney disease, indicated that Jag1 and Notch2 levels were higher in all analyzed kidney fibrosis models. Mice with tubule-specific deletion of Jag1 or Notch2 (Kspcre/Jag1flox/floxand Kspcre/Notch2flox/flox) had no kidney-specific alterations at baseline but showed protection from FA-induced kidney fibrosis. Tubule-specific genetic deletion of Notch1 and global knockout of Notch3 had no effect on fibrosis. In vitro chromatin immunoprecipitation experiments and genome-wide expression studies identified the mitochondrial transcription factor A (Tfam) as a direct Notch target. Re-expression of Tfam in tubule cells prevented Notch-induced metabolic and profibrotic reprogramming. Tubule–specific deletion of Tfam resulted in fibrosis. In summary, Jag1 and Notch2 play a key role in kidney fibrosis development by regulating Tfam expression and metabolic reprogramming. AU - Huang, S.* AU - Park, J.* AU - Qiu, C.* AU - Chung, K.F.* AU - Li, S.Y.* AU - Sirin, Y.* AU - Han, S.H.* AU - Taylor, V.* AU - Zimber-Strobl, U. AU - Susztak, K.* C1 - 54332 C2 - 45524 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - Jagged1/Notch2 controls kidney fibrosis via Tfam-mediated metabolic reprogramming. JO - PLoS Biol. VL - 16 IS - 9 PB - Public Library Science PY - 2018 SN - 1544-9173 ER - TY - JOUR AB - Directional mechanoreception by hair cells is transmitted to the brain via afferent neurons to enable postural control and rheotaxis. Neuronal tuning to individual directions of mechanical flow occurs when each peripheral axon selectively synapses with multiple hair cells of identical planar polarization. How such mechanosensory labeled lines are established and maintained remains unsolved. Here, we use the zebrafish lateral line to reveal that asymmetric activity of the transcription factor Emx2 diversifies hair cell identity to instruct polarity-selective synaptogenesis. Unexpectedly, presynaptic scaffolds and coherent hair cell orientation are dispensable for synaptic selectivity, indicating that epithelial planar polarity and synaptic partner matching are separable. Moreover, regenerating axons recapitulate synapses with hair cells according to Emx2 expression but not global orientation. Our results identify a simple cellular algorithm that solves the selectivity task even in the presence of noise generated by the frequent receptor cell turnover. They also suggest that coupling connectivity patterns to cellular identity rather than polarity relaxes developmental and evolutionary constraints to innervation of organs with differing orientation. AU - Lozano-Ortega, M. AU - Valera, G. AU - Xiao, Y. AU - Faucherre, A.* AU - López-Schier, H. C1 - 53968 C2 - 45155 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - Hair cell identity establishes labeled lines of directional mechanosensation. JO - PLoS Biol. VL - 16 IS - 7 PB - Public Library Science PY - 2018 SN - 1544-9173 ER - TY - JOUR AB - Head and neck squamous cell carcinomas (HNSCCs) are characterized by outstanding molecular heterogeneity that results in severe therapy resistance and poor clinical outcome. Inter- and intratumoral heterogeneity in epithelial-mesenchymal transition (EMT) was recently revealed as a major parameter of poor clinical outcome. Here, we addressed the expression and function of the therapeutic target epidermal growth factor receptor (EGFR) and of the major determinant of epithelial differentiation epithelial cell adhesion molecule (EpCAM) in clinical samples and in vitro models of HNSCCs. We describe improved survival of EGFRlow/EpCAMhighHNSCC patients (n = 180) and provide a molecular basis for the observed disparities in clinical outcome. EGF/EGFR have concentration-dependent dual capacities as inducers of proliferation and EMT through differential activation of the central molecular switch phosphorylated extracellular signal–regulated kinase 1/2 (pERK1/2) and EMT transcription factors (EMT-TFs) Snail, zinc finger E-box-binding homeobox 1 (Zeb1), and Slug. Furthermore, soluble ectodomain of EpCAM (EpEX) was identified as a ligand of EGFR that activates pERK1/2 and phosphorylated AKT (pAKT) and induces EGFR-dependent proliferation but represses EGF-mediated EMT, Snail, Zeb1, and Slug activation and cell migration. EMT repression by EpEX is realized through competitive modulation of pERK1/2 activation strength and inhibition of EMT-TFs, which is reflected in levels of pERK1/2 and its target Slug in clinical samples. Accordingly, high expression of pERK1/2 and/or Slug predicted poor outcome of HNSCCs. Hence, EpEX is a ligand of EGFR that induces proliferation but counteracts EMT mediated by the EGF/EGFR/pERK1/2 axis. Therefore, the emerging EGFR/EpCAM molecular cross talk represents a promising target to improve patient-tailored adjuvant treatment of HNSCCs. AU - Pan, M.* AU - Schinke, H.* AU - Luxenburger, E.* AU - Kranz, G.* AU - Shakhtour, J.* AU - Libl, D.* AU - Huang, Y.* AU - Gaber, A.* AU - Pavšič, M.* AU - Lenarčič, B.* AU - Kitz, J.* AU - Jakob, M.* AU - Schwenk-Zieger, S.* AU - Canis, M.* AU - Hess J. AU - Unger, K. AU - Baumeister, P. AU - Gires, O. C1 - 54496 C2 - 45588 CY - 1160 Battery Street, Ste 100, San Francisco, Ca 94111 Usa TI - EpCAM ectodomain EpEX is a ligand of EGFR that counteracts EGF-mediated epithelial-mesenchymal transition through modulation of phospho-ERK1/2 in head and neck cancers. JO - PLoS Biol. VL - 16 IS - 9 PB - Public Library Science PY - 2018 SN - 1544-9173 ER - TY - JOUR AB - In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines. AU - McMurry, J.A.* AU - Juty, N.* AU - Blomberg, N.* AU - Burdett, T.* AU - Conlin, T.* AU - Conte, N.* AU - Courtot, M.* AU - Deck, J.* AU - Dumontier, M.* AU - Fellows, D.K.* AU - Gonzalez-Beltran, A.* AU - Gormanns, P. AU - Grethe, J.* AU - Hastings, J.* AU - Hériché, J.K.* AU - Hermjakob, H.* AU - Ison, J.C.* AU - Jimenez, R.C.* AU - Jupp, S.* AU - Kunze, J.* AU - Laibe, C.* AU - Le Novère, N.* AU - Malone, J.* AU - Martin, M.J.* AU - McEntyre, J.R.* AU - Morris, C.* AU - Muilu, J.* AU - Müller, W.* AU - Rocca-Serra, P.* AU - Sansone, S.A.* AU - Sariyar, M.* AU - Snoep, J.L.* AU - Soiland-Reyes, S.* AU - Stanford, N.J.* AU - Swainston, N.* AU - Washington, N.* AU - Williams, A.R.* AU - Wimalaratne, S.M.* AU - Winfree, L.M.* AU - Wolstencroft, K.* AU - Goble, C.* AU - Mungall, C.J.* AU - Haendel, M.A.* AU - Parkinson, H.* C1 - 51445 C2 - 43237 CY - San Francisco TI - Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. JO - PLoS Biol. VL - 15 IS - 6 PB - Public Library Science PY - 2017 SN - 1544-9173 ER - TY - JOUR AB - During development, progenitor expansion, lineage allocation, and implementation of differentiation programs need to be tightly coordinated so that different cell types are generated in the correct numbers for appropriate tissue size and function. Pancreatic dysfunction results in some of the most debilitating and fatal diseases, including pancreatic cancer and diabetes. Several transcription factors regulating pancreas lineage specification have been identified, and Notch signalling has been implicated in lineage allocation, but it remains unclear how these processes are coordinated. Using a combination of genetic approaches, organotypic cultures of embryonic pancreata, and genomics, we found that sphingosine-1-phosphate (S1p), signalling through the G protein coupled receptor (GPCR) S1pr2, plays a key role in pancreas development linking lineage allocation and specification. S1pr2 signalling promotes progenitor survival as well as acinar and endocrine specification. S1pr2-mediated stabilisation of the yes-associated protein (YAP) is essential for endocrine specification, thus linking a regulator of progenitor growth with specification. YAP stabilisation and endocrine cell specification rely on Gαi subunits, revealing an unexpected specificity of selected GPCR intracellular signalling components. Finally, we found that S1pr2 signalling posttranscriptionally attenuates Notch signalling levels, thus regulating lineage allocation. Both S1pr2-mediated YAP stabilisation and Notch attenuation are necessary for the specification of the endocrine lineage. These findings identify S1p signalling as a novel key pathway coordinating cell survival, lineage allocation, and specification and linking these processes by regulating YAP levels and Notch signalling. Understanding lineage allocation and specification in the pancreas will shed light in the origins of pancreatic diseases and may suggest novel therapeutic approaches. AU - Serafimidis, I.* AU - Rodriguez-Aznar, E. AU - Lesche, M.* AU - Yoshioka, K.* AU - Takuwa, Y.* AU - Dahl, A.* AU - Pan, D.* AU - Gavalas, A. C1 - 50610 C2 - 42425 TI - Pancreas lineage allocation and specification are regulated by sphingosine-1-phosphate signalling. JO - PLoS Biol. VL - 15 IS - 3 PY - 2017 SN - 1544-9173 ER - TY - JOUR AB - The Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines were developed to address the lack of reproducibility in biomedical animal studies and improve the communication of research findings. While intended to guide the preparation of peer-reviewed manuscripts, the principles of transparent reporting are also fundamental for in vivo databases. Here, we describe the benefits and challenges of applying the guidelines for the International Mouse Phenotyping Consortium (IMPC), whose goal is to produce and phenotype 20,000 knockout mouse strains in a reproducible manner across ten research centres. In addition to ensuring the transparency and reproducibility of the IMPC, the solutions to the challenges of applying the ARRIVE guidelines in the context of IMPC will provide a resource to help guide similar initiatives in the future. AU - Karp, N.A.* AU - Meehan, T.F.* AU - Morgan, H.* AU - Mason, J.C.* AU - Blake, A.* AU - Kurbatova, N.* AU - Smedley, D.* AU - Jacobsen, J.* AU - Mott, R.F.* AU - Iyer, V.* AU - Matthews, P.* AU - Melvin, D.G.* AU - Wells, S.* AU - Flenniken, A.M.* AU - Masuya, H.* AU - Wakana, S.* AU - White, J.K.* AU - Lloyd, K.C.K.* AU - Reynolds, C.L.* AU - Paylor, R.* AU - West, D.B.* AU - Svenson, K.L.* AU - Chesler, E.J.* AU - Hrabě de Angelis, M. AU - Tocchini-Valentini, G.P.* AU - Sorg, T.* AU - Herault, Y.* AU - Parkinson, H.* AU - Mallon, A.M.* AU - Brown, S.D.* C1 - 44900 C2 - 37069 CY - San Francisco TI - Applying the ARRIVE guidelines to an in vivo database. JO - PLoS Biol. VL - 13 IS - 5 PB - Public Library Science PY - 2015 SN - 1544-9173 ER - TY - JOUR AB - Metazoans display remarkable conservation of gene families, including growth factors, yet somehow these genes are used in different ways to generate tremendous morphological diversity. While variations in the magnitude and spatio-temporal aspects of signaling by a growth factor can generate different body patterns, how these signaling variations are organized and coordinated during development is unclear. Basic body plans are organized by the end of gastrulation and are refined as limbs, organs, and nervous systems co-develop. Despite their proximity to developing tissues, neurons are primarily thought to act after development, on behavior. Here, we show that in Caenorhabditis elegans, the axonal projections of neurons regulate tissue progenitor responses to Wnts so that certain organs develop with the correct morphology at the right axial positions. We find that foreshortening of the posteriorly directed axons of the two canal-associated neurons (CANs) disrupts mid-body vulval morphology, and produces ectopic vulval tissue in the posterior epidermis, in a Wnt-dependent manner. We also provide evidence that suggests that the posterior CAN axons modulate the location and strength of Wnt signaling along the anterior-posterior axis by employing a Ror family Wnt receptor to bind posteriorly derived Wnts, and hence, refine their distributions. Surprisingly, despite high levels of Ror expression in many other cells, these cells cannot substitute for the CAN axons in patterning the epidermis, nor can cells expressing a secreted Wnt inhibitor, SFRP-1. Thus, unmyelinated axon tracts are critical for patterning the C. elegans body. Our findings suggest that the evolution of neurons not only improved metazoans by increasing behavioral complexity, but also by expanding the diversity of developmental patterns generated by growth factors such as Wnts. AU - Modzelewska, K.* AU - Lauritzen, A.* AU - Hasenöder, S. AU - Brown, L.* AU - Georgiou, J.* AU - Moghal, N.* C1 - 26184 C2 - 32111 TI - Neurons refine the Caenorhabditis elegans body plan by directing axial patterning by Wnts. JO - PLoS Biol. VL - 11 IS - 1 PB - Public Library of Science PY - 2013 SN - 1544-9173 ER - TY - JOUR AB - Hypothalamic neurons are main regulators of energy homeostasis. Neuronal function essentially depends on plasma membrane-located gangliosides. The present work demonstrates that hypothalamic integration of metabolic signals requires neuronal expression of glucosylceramide synthase (GCS; UDP-glucose:ceramide glucosyltransferase). As a major mechanism of central nervous system (CNS) metabolic control, we demonstrate that GCS-derived gangliosides interacting with leptin receptors (ObR) in the neuronal membrane modulate leptin-stimulated formation of signaling metabolites in hypothalamic neurons. Furthermore, ganglioside-depleted hypothalamic neurons fail to adapt their activity (c-Fos) in response to alterations in peripheral energy signals. Consequently, mice with inducible forebrain neuron-specific deletion of the UDP-glucose:ceramide glucosyltransferase gene (Ugcg) display obesity, hypothermia, and lower sympathetic activity. Recombinant adeno-associated virus (rAAV)-mediated Ugcg delivery to the arcuate nucleus (Arc) significantly ameliorated obesity, specifying gangliosides as seminal components for hypothalamic regulation of body energy homeostasis. AU - Nordström, V.* AU - Willershäuser, M. AU - Herzer, S.* AU - Rozman, J. AU - von Bohlen und Halbach, O.* AU - Meldner, S.* AU - Rothermel, U.* AU - Kaden, S.* AU - Roth, F. C.* AU - Waldeck, C.* AU - Gertz, N.* AU - Hrabě de Angelis, M. AU - Draguhn, A.* AU - Klingenspor, M.* AU - Gröne, H. J.* AU - Jennemann, R.* C1 - 23624 C2 - 31217 TI - Neuronal expression of glucosylceramide synthase in central nervous system regulates body weight and energy homeostasis. JO - PLoS Biol. VL - 11 IS - 3 PB - Public Library of Science PY - 2013 SN - 1544-9173 ER - TY - JOUR AB - Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members--that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses ("variolation" or "inoculation"). AU - Konrad, M.* AU - Vyleta, M.L.* AU - Theis, F.J. AU - Stock, M.* AU - Tragust, S.* AU - Klatt, M.* AU - Drescher, V.* AU - Marr, C. AU - Ugelvig, L.V.* AU - Cremer, S.* C1 - 7915 C2 - 29915 TI - Social transfer of pathogenic fungus promotes active immunisation in ant colonies. JO - PLoS Biol. VL - 10 IS - 4 PB - Public Library of Science PY - 2012 SN - 1544-9173 ER - TY - JOUR AB - The tumor necrosis factor-receptor-associated factor 2 (TRAF2)- and Nck-interacting kinase (TNIK) is a ubiquitously expressed member of the germinal center kinase family. The TNIK functions in hematopoietic cells and the role of TNIK-TRAF interaction remain largely unknown. By functional proteomics we identified TNIK as interaction partner of the latent membrane protein 1 (LMP1) signalosome in primary human B-cells infected with the Epstein-Barr tumor virus (EBV). RNAi-mediated knockdown proved a critical role for TNIK in canonical NF-κB and c-Jun N-terminal kinase (JNK) activation by the major EBV oncoprotein LMP1 and its cellular counterpart, the B-cell co-stimulatory receptor CD40. Accordingly, TNIK is mandatory for proliferation and survival of EBV-transformed B-cells. TNIK forms an activation-induced complex with the critical signaling mediators TRAF6, TAK1/TAB2, and IKKβ, and mediates signalosome formation at LMP1. TNIK directly binds TRAF6, which bridges TNIK's interaction with the C-terminus of LMP1. Separate TNIK domains are involved in NF-κB and JNK signaling, the N-terminal TNIK kinase domain being essential for IKKβ/NF-κB and the C-terminus for JNK activation. We therefore suggest that TNIK orchestrates the bifurcation of both pathways at the level of the TRAF6-TAK1/TAB2-IKK complex. Our data establish TNIK as a novel key player in TRAF6-dependent JNK and NF-κB signaling and a transducer of activating and transforming signals in human B-cells. AU - Shkoda, A. AU - Town, J.A. AU - Griese, J. AU - Romio, M. AU - Sarioglu, H. AU - Knöfel, T. AU - Giehler, F. AU - Kieser, A. C1 - 8380 C2 - 30089 TI - The germinal center kinase TNIK is required for canonical NF-κB and JNK signaling in B-cells by the EBV oncoprotein LMP1 and the CD40 receptor. JO - PLoS Biol. VL - 10 IS - 8 PB - Public Library of Science PY - 2012 SN - 1544-9173 ER - TY - JOUR AB - The initiation, execution, and completion of complex locomotor behaviors are depending on precisely integrated neural circuitries consisting of motor pathways that activate muscles in the extremities and sensory afferents that deliver feedback to motoneurons. These projections form in tight temporal and spatial vicinities during development, yet the molecular mechanisms and cues coordinating these processes are not well understood. Using cell-type specific ablation of the axon guidance receptor Neuropilin-1 (Npn-1) in spinal motoneurons or in sensory neurons in the dorsal root ganglia (DRG), we have explored the contribution of this signaling pathway to correct innervation of the limb. We show that Npn-1 controls the fasciculation of both projections and mediates inter-axonal communication. Removal of Npn-1 from sensory neurons results in defasciculation of sensory axons and, surprisingly, also of motor axons. In addition, the tight coupling between these two heterotypic axonal populations is lifted with sensory fibers now leading the spinal nerve projection. These findings are corroborated by partial genetic elimination of sensory neurons, which causes defasciculation of motor projections to the limb. Deletion of Npn-1 from motoneurons leads to severe defasciculation of motor axons in the distal limb and dorsal-ventral pathfinding errors, while outgrowth and fasciculation of sensory trajectories into the limb remain unaffected. Genetic elimination of motoneurons, however, revealed that sensory axons need only minimal scaffolding by motor axons to establish their projections in the distal limb. Thus, motor and sensory axons are mutually dependent on each other for the generation of their trajectories and interact in part through Npn-1-mediated fasciculation before and within the plexus region of the limbs. AU - Hüttl, R.E. AU - Soellner, H. AU - Bianchi, E. AU - Novitch, B.G.* AU - Huber, A.B. C1 - 6517 C2 - 28842 TI - Npn-1 contributes to axon-axon interactions that differentially control sensory and motor innervation of the limb. JO - PLoS Biol. VL - 9 IS - 2 PB - Public Library of Science PY - 2011 SN - 1544-9173 ER - TY - JOUR AB - In eukaryotes, hundreds of mRNAs are localized by specialized transport complexes. For localization, transcripts are recognized by RNA-binding proteins and incorporated into motor-containing messenger ribonucleoprotein particles (mRNPs). To date, the molecular assembly of such mRNPs is not well understood and most details on cargo specificity remain unresolved. We used ASH1-mRNA transport in yeast to provide a first assessment of where and how localizing mRNAs are specifically recognized and incorporated into mRNPs. By using in vitro-interaction and reconstitution assays, we found that none of the implicated mRNA-binding proteins showed highly specific cargo binding. Instead, we identified the cytoplasmic myosin adapter She3p as additional RNA-binding protein. We further found that only the complex of the RNA-binding proteins She2p and She3p achieves synergistic cargo binding, with an at least 60-fold higher affinity for localizing mRNAs when compared to control RNA. Mutational studies identified a C-terminal RNA-binding fragment of She3p to be important for synergistic RNA binding with She2p. The observed cargo specificity of the ternary complex is considerably higher than previously reported for localizing mRNAs. It suggests that RNA binding for mRNP localization generally exhibits higher selectivity than inferred from previous in vitro data. This conclusion is fully consistent with a large body of in vivo evidence from different organisms. Since the ternary yeast complex only assembles in the cytoplasm, specific mRNA recognition might be limited to the very last steps of mRNP assembly. Remarkably, the mRNA itself triggers the assembly of mature, motor-containing complexes. Our reconstitution of a major portion of the mRNA-transport complex offers new and unexpected insights into the molecular assembly of specific, localization-competent mRNPs and provides an important step forward in our mechanistic understanding of mRNA localization in general. AU - Müller, M. AU - Heym, R.G. AU - Meyer, A.* AU - Kramer, K.* AU - Schmid, M.* AU - Cramer, P.* AU - Urlaub, H.* AU - Jansen, R.P.* AU - Niessing, D. C1 - 6549 C2 - 28861 TI - A cytoplasmic complex mediates specific mRNA recognition and localization in yeast. JO - PLoS Biol. VL - 9 IS - 4 PB - Public Library of Science PY - 2011 SN - 1544-9173 ER - TY - JOUR AB - The mechanisms underlying the selective death of substantia nigra (SN) neurons in Parkinson disease (PD) remain elusive. While inactivation of DJ-1, an oxidative stress suppressor, causes PD, animal models lacking DJ-1 show no overt dopaminergic (DA) neuron degeneration in the SN. Here, we show that aging mice lacking DJ-1 and the GDNF-receptor Ret in the DA system display an accelerated loss of SN cell bodies, but not axons, compared to mice that only lack Ret signaling. The survival requirement for DJ-1 is specific for the GIRK2-positive subpopulation in the SN which projects exclusively to the striatum and is more vulnerable in PD. Using Drosophila genetics, we show that constitutively active Ret and associated Ras/ERK, but not PI3K/Akt, signaling components interact genetically with DJ-1. Double loss-of-function experiments indicate that DJ-1 interacts with ERK signaling to control eye and wing development. Our study uncovers a conserved interaction between DJ-1 and Ret-mediated signaling and a novel cell survival role for DJ-1 in the mouse. A better understanding of the molecular connections between trophic signaling, cellular stress and aging could uncover new targets for drug development in PD. AU - Aron, L.* AU - Klein, P.* AU - Pham, T.T. AU - Kramer, E.R.* AU - Wurst, W. AU - Klein, R.* C1 - 1481 C2 - 27179 CY - San Francisco TI - Pro-survival role for Parkinson's associated gene DJ-1 revealed in trophically impaired dopaminergic neurons. JO - PLoS Biol. VL - 8 IS - 4 PB - Public Library of Science PY - 2010 SN - 1544-9173 ER - TY - JOUR AB - Astroglia from the postnatal cerebral cortex can be reprogrammed in vitro to generate neurons following forced expression of neurogenic transcription factors, thus opening new avenues towards a potential use of endogenous astroglia for brain repair. However, in previous attempts astroglia-derived neurons failed to establish functional synapses, a severe limitation towards functional neurogenesis. It remained therefore also unknown whether neurons derived from reprogrammed astroglia could be directed towards distinct neuronal subtype identities by selective expression of distinct neurogenic fate determinants. Here we show that strong and persistent expression of neurogenic fate determinants driven by silencing-resistant retroviral vectors instructs astroglia from the postnatal cortex in vitro to mature into fully functional, synapse-forming neurons. Importantly, the neurotransmitter fate choice of astroglia-derived neurons can be controlled by selective expression of distinct neurogenic transcription factors: forced expression of the dorsal telencephalic fate determinant neurogenin-2 (Neurog2) directs cortical astroglia to generate synapse-forming glutamatergic neurons; in contrast, the ventral telencephalic fate determinant Dlx2 induces a GABAergic identity, although the overall efficiency of Dlx2-mediated neuronal reprogramming is much lower compared to Neurog2, suggesting that cortical astroglia possess a higher competence to respond to the dorsal telencephalic fate determinant. Interestingly, however, reprogramming of astroglia towards the generation of GABAergic neurons was greatly facilitated when the astroglial cells were first expanded as neurosphere cells prior to transduction with Dlx2. Importantly, this approach of expansion under neurosphere conditions and subsequent reprogramming with distinct neurogenic transcription factors can also be extended to reactive astroglia isolated from the adult injured cerebral cortex, allowing for the selective generation of glutamatergic or GABAergic neurons. These data provide evidence that cortical astroglia can undergo a conversion across cell lineages by forced expression of a single neurogenic transcription factor, stably generating fully differentiated neurons. Moreover, neuronal reprogramming of astroglia is not restricted to postnatal stages but can also be achieved from terminally differentiated astroglia of the adult cerebral cortex following injury-induced reactivation. AU - Heinrich, C. AU - Blum, R.* AU - Gascón, S. AU - Masserdotti, G.* AU - Tripathi, P. AU - Sánchez, R.* AU - Tiedt, S.* AU - Schroeder, T. AU - Götz, M. AU - Berninger, B. C1 - 107 C2 - 27217 TI - Directing astroglia from the cerebral cortex into subtype specific functional neurons. JO - PLoS Biol. VL - 8 IS - 5 PB - Public Library of Science PY - 2010 SN - 1544-9173 ER - TY - JOUR AB - Ischemic stroke is the second leading cause of death worldwide. Only one moderately effective therapy exists, albeit with contraindications that exclude 90% of the patients. This medical need contrasts with a high failure rate of more than 1,000 pre-clinical drug candidates for stroke therapies. Thus, there is a need for translatable mechanisms of neuroprotection and more rigid thresholds of relevance in pre-clinical stroke models. One such candidate mechanism is oxidative stress. However, antioxidant approaches have failed in clinical trials, and the significant sources of oxidative stress in stroke are unknown. We here identify NADPH oxidase type 4 (NOX4) as a major source of oxidative stress and an effective therapeutic target in acute stroke. Upon ischemia, NOX4 was induced in human and mouse brain. Mice deficient in NOX4 (Nox4(-/-)) of either sex, but not those deficient for NOX1 or NOX2, were largely protected from oxidative stress, blood-brain-barrier leakage, and neuronal apoptosis, after both transient and permanent cerebral ischemia. This effect was independent of age, as elderly mice were equally protected. Restoration of oxidative stress reversed the stroke-protective phenotype in Nox4(-/-) mice. Application of the only validated low-molecular-weight pharmacological NADPH oxidase inhibitor, VAS2870, several hours after ischemia was as protective as deleting NOX4. The extent of neuroprotection was exceptional, resulting in significantly improved long-term neurological functions and reduced mortality. NOX4 therefore represents a major source of oxidative stress and novel class of drug target for stroke therapy. AU - Kleinschnitz, C.* AU - Grund, H.* AU - Wingler, K.* AU - Armitage, M.E.* AU - Jones, E.* AU - Mittal, M.* AU - Barit, D.* AU - Schwarz, T.* AU - Geis, C.* AU - Kraft, P.* AU - Barthel, K.* AU - Schuhmann, M.K.* AU - Herrmann, A.M.* AU - Meuth, S.G.* AU - Stoll, G.* AU - Meurer, S.* AU - Schrewe, A. AU - Becker, L. AU - Gailus-Durner, V. AU - Fuchs, H. AU - Klopstock, T.* AU - Hrabě de Angelis, M. AU - Jandeleit-Dahm, K.* AU - Shah, A.M.* AU - Weissmann, N.* AU - Schmidt, H.H.* C1 - 4929 C2 - 27431 TI - Post-stroke inhibition of induced NADPH oxidase type 4 prevents oxidative stress and neurodegeneration. JO - PLoS Biol. VL - 8 IS - 9 PB - Public Library Science PY - 2010 SN - 1544-9173 ER - TY - JOUR AB - Long distance migration of differentiating granule cells from the cerebellar upper rhombic lip has been reported in many vertebrates. However, the knowledge about the subcellular dynamics and molecular mechanisms regulating directional neuronal migration in vivo is just beginning to emerge. Here we show by time-lapse imaging in live zebrafish (Danio rerio) embryos that cerebellar granule cells migrate in chain-like structures in a homotypic glia-independent manner. Temporal rescue of zebrafish Cadherin-2 mutants reveals a direct role for this adhesion molecule in mediating chain formation and coherent migratory behavior of granule cells. In addition, Cadherin-2 maintains the orientation of cell polarization in direction of migration, whereas in Cadherin-2 mutant granule cells the site of leading edge formation and centrosome positioning is randomized. Thus, the lack of adhesion leads to impaired directional migration with a mispositioning of Cadherin-2 deficient granule cells as a consequence. Furthermore, these cells fail to differentiate properly into mature granule neurons. In vivo imaging of Cadherin-2 localization revealed the dynamics of this adhesion molecule during cell locomotion. Cadherin-2 concentrates transiently at the front of granule cells during the initiation of individual migratory steps by intramembraneous transport. The presence of Cadherin-2 in the leading edge corresponds to the observed centrosome orientation in direction of migration. Our results indicate that Cadherin-2 plays a key role during zebrafish granule cell migration by continuously coordinating cell-cell contacts and cell polarity through the remodeling of adherens junctions. As Cadherin-containing adherens junctions have been shown to be connected via microtubule fibers with the centrosome, our results offer an explanation for the mechanism of leading edge and centrosome positioning during nucleokinetic migration of many vertebrate neuronal populations. AU - Rieger, S. AU - Senghaas, N. AU - Walch, A.K. AU - Köster, R.W. C1 - 334 C2 - 26738 TI - Cadherin-2 controls directional chain migration of cerebellar granule neurons. JO - PLoS Biol. VL - 7 IS - 11 PB - Public Library of Science PY - 2009 SN - 1544-9173 ER - TY - JOUR AB - Newborn granule cells become functionally integrated into the synaptic circuitry of the adult dentate gyrus after a morphological and electrophysiological maturation process. The molecular mechanisms by which immature neurons and the neurites extending from them find their appropriate position and target area remain largely unknown. Here we show that single-cell-specific knockdown of cyclin-dependent kinase 5 (cdk5) activity in newborn cells using a retrovirus-based strategy leads to aberrant growth of dendritic processes, which is associated with an altered migration pattern of newborn cells. Even though spine formation and maturation are reduced in cdk5-deficient cells, aberrant dendrites form ectopic synapses onto hilar neurons. These observations identify cdk5 to be critically involved in the maturation and dendrite extension of newborn neurons in the course of adult neurogenesis. The data presented here also suggest a mechanistic dissociation between accurate dendritic targeting and subsequent synapse formation. AU - Jessberger, S.* AU - Aigner, S.* AU - Clemenson, G.* AU - Toni, N.* AU - Lie, D.C.* AU - Karalay, O.* AU - Overall, R.* AU - Kempermann, G.* AU - Gage, F.* C1 - 3318 C2 - 25800 SP - 2465-2475 TI - Cdk5 regulates accurate maturation of newborn granule cells in the adult hippocampus. JO - PLoS Biol. VL - 6 IS - 11 PB - Public Library of Science PY - 2008 SN - 1544-9173 ER - TY - JOUR AB - The tumor necrosis factor (TNF)-receptor 1-associated death domain protein (TRADD) mediates induction of apoptosis as well as activation of NF-kappaB by cellular TNF-receptor 1 (TNFR1). TRADD is also recruited by the latent membrane protein 1 (LMP1) oncoprotein of Epstein-Barr virus, but its role in LMP1 signaling has remained enigmatic. In human B lymphocytes, we have generated, to our knowledge, the first genetic knockout of TRADD to investigate TRADD's role in LMP1 signal transduction. Our data from TRADD-deficient cells demonstrate that TRADD is a critical signaling mediator of LMP1 that is required for LMP1 to recruit and activate I-kappaB kinase beta (IKKbeta). However, in contrast to TNFR1, LMP1-induced TRADD signaling does not induce apoptosis. Searching for the molecular basis for this observation, we characterized the 16 C-terminal amino acids of LMP1 as an autonomous and unique virus-derived TRADD-binding domain. Replacing the death domain of TNFR1 by LMP1's TRADD-binding domain converts TNFR1 into a nonapoptotic receptor that activates NF-kappaB through a TRAF6-dependent pathway, like LMP1 but unlike wild-type TNFR1. Thus, the unique interaction of LMP1 with TRADD encodes the transforming phenotype of viral TRADD signaling and masks TRADD's pro-apoptotic function. AU - Schneider, F. AU - Neugebauer, J. AU - Griese, J. AU - Liefold, N. AU - Kutz, H. AU - Briseño, C. AU - Kieser, A. C1 - 2562 C2 - 25113 SP - 86-98 TI - The viral oncoprotein LMP1 exploits TRADD for signaling by masking its apoptotic activity. JO - PLoS Biol. VL - 6 IS - 1 PB - Public Library of Science PY - 2008 SN - 1544-9173 ER - TY - JOUR AB - Proliferating cell nuclear antigen ( PCNA) is a DNA polymerase cofactor and regulator of replication-linked functions. Upon DNA damage, yeast and vertebrate PCNA is modified at the conserved lysine K164 by ubiquitin, which mediates error-prone replication across lesions via translesion polymerases. We investigated the role of PCNA ubiquitination in variants of the DT40 B cell line that are mutant in K164 of PCNA or in Rad18, which is involved in PCNA ubiquitination. Remarkably, the PCNA(K164R) mutation not only renders cells sensitive to DNA-damaging agents, but also strongly reduces activation induced deaminase-dependent single-nucleotide substitutions in the immunoglobulin light-chain locus. This is the first evidence, to our knowledge, that vertebrates exploit the PCNA-ubiquitin pathway for immunoglobulin hypermutation, most likely through the recruitment of error-prone DNA polymerases. AU - Arakawa, H. AU - Moldovan, G.-L.* AU - Saribasak, H.* AU - Saribasak, N.N. AU - Jentsch, S.* AU - Buerstedde, J.-M. C1 - 2359 C2 - 24150 SP - 1947-1956 TI - A role for PCNA ubiquitination in immunoglobulin hypermutation. JO - PLoS Biol. VL - 4 IS - 11 PB - Public Library of Science PY - 2006 SN - 1544-9173 ER - TY - JOUR AB - DNA viruses such as herpesviruses are known to encode homologs of cellular antiapoptotic viral Bcl-2 proteins (vBcl2s), which protect the virus from apoptosis in its host cell during virus synthesis. Epstein-Barr virus (EBV), a human tumor virus and a prominent member of gamma-herpesviruses, infects primary resting B lymphocytes to establish a latent infection and yield proliferating, growth-transformed B cells in vitro. In these cells, 11 viral genes that contribute to cellular transformation are consistently expressed. EBV also encodes two vBcl-2 genes whose roles are unclear. Here we show that the genetic inactivation of both vBcl-2 genes disabled EBV's ability to transform primary resting B lymphocytes. Primary B cells infected with a vBcl-2-negative virus did not enter the cell cycle and died of immediate apoptosis. Apoptosis was abrogated in infected cells in which vBcl-2 genes were maximally expressed within the first 24 h postinfection. During latent infection, however, the expression of vBcl-2 genes became undetectable. Thus, both vBcl-2 homologs are essential for initial cellular transformation but become dispensable once a latent infection is established. Because long-lived, latently infected memory B cells and EBV-associated B-cell lymphomas are derived from EBV-infected proapoptotic germinal center B cells, we conclude that vBcl-2 genes are essential for the initial evasion of apoptosis in cells in vivo in which the virus establishes a latent infection or causes cellular transformation or both. AU - Altmann, M. AU - Hammerschmidt, W. C1 - 2753 C2 - 23212 SP - 2148-2157 TI - Epstein-Barr Virus provides a new paradigm: A requirement for the immediate inhibition of apoptosis. JO - PLoS Biol. VL - 3 IS - 12 PB - Public Library of Science PY - 2005 SN - 1544-9173 ER - TY - JOUR AB - Studies of higher-order chromatin arrangements are an essential part of ongoing attempts to explore changes in epigenome structure and their functional implications during development and cell differentiation. However, the extent and cell-type-specificity of three-dimensional (3D) chromosome arrangements has remained controversial. In order to overcome technical limitations of previous studies, we have developed tools that allow the quantitative 3D positional mapping of all chromosomes simultaneously. We present unequivocal evidence for a probabilistic 3D order of prometaphase chromosomes, as well as of chromosome territories (CTs) in nuclei of quiescent (G0) and cycling (early S-phase) human diploid fibroblasts (46, XY). Radial distance measurements showed a probabilistic, highly nonrandom correlation with chromosome size: small chromosomes-independently of their gene density-were distributed significantly closer to the center of the nucleus or prometaphase rosette, while large chromosomes were located closer to the nuclear or rosette rim. This arrangement was independently confirmed in both human fibroblast and amniotic fluid cell nuclei. Notably, these cell types exhibit flat-ellipsoidal cell nuclei, in contrast to the spherical nuclei of lymphocytes and several other human cell types, for which we and others previously demonstrated gene-density-correlated radial 3D CT arrangements. Modeling of 3D CT arrangements suggests that cell-type-specific differences in radial CT arrangements are not solely due to geometrical constraints that result from nuclear shape differences. We also found gene-density-correlated arrangements of higher-order chromatin shared by all human cell types studied so far. Chromatin domains, which are gene-poor, form a layer beneath the nuclear envelope, while gene-dense chromatin is enriched in the nuclear interior. We discuss the possible functional implications of this finding. AU - Bolzer, A.* AU - Kreth, G.* AU - Solovei, I.* AU - Koehler, D.* AU - Saracoglu, K.* AU - Fauth, C. AU - Müller, S.* AU - Eils, R.* AU - Cremer, C.* AU - Speicher, M.R. AU - Cremer, T.* C1 - 4479 C2 - 23184 SP - 826-842 TI - Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosetts. JO - PLoS Biol. VL - 3 IS - 5 PB - Public Library of Science PY - 2005 SN - 1544-9173 ER - TY - JOUR AB - Abnormalities of chromosome number are frequently observed in cancers. The mechanisms regulating chromosome segregation in human cells are therefore of great interest. Recently it has been reported that human cells without an hSecurin gene lose chromosomes at a high frequency. Here we show that, after hSecurin knockout through homologous recombination, chromosome losses are only a short, transient effect. After a few passages hSecurin(-/-) cells became chromosomally stable and executed mitoses normally. This was unexpected, as the securin loss resulted in a persisting reduction of the sister-separating protease separase and inefficient cleavage of the cohesin subunit Scc1. Our data demonstrate that securin is dispensable for chromosomal stability in human cells. We propose that human cells possess efficient mechanisms to compensate for the loss of genes involved in chromosome segregation. AU - Pfleghaar, K.* AU - Heubes, S.* AU - Cox, J.* AU - Stemmann, O.* AU - Speicher, M.R. C1 - 3287 C2 - 23081 SP - 2127-2134 TI - Securin is not required for chromosomal stability in human cells. JO - PLoS Biol. VL - 3 IS - 12 PB - Public Library of Science PY - 2005 SN - 1544-9173 ER - TY - JOUR AB - Depending on the species and the lymphoid organ, activation-induced cytidine deaminase (AID) expression triggers diversification of the rearranged immunoglobulin (Ig) genes by pseudo V (psiV) gene- templated gene conversion or somatic hypermutation. To investigate how AID can alternatively induce recombination or hypermutation, psiV gene deletions were introduced into the rearranged light chain locus of the DT40 B-cell line. We show that the stepwise removal of the psiV donors not only reduces and eventually abolishes Ig gene conversion, but also activates AID-dependent Ig hypermutation. This strongly supports a model in which AID induces a common modification in the rearranged V(D)J segment, leading to a conversion tract in the presence of nearby donor sequences and to a point mutation in their absence. AU - Arakawa, H. AU - Saribasak, H. AU - Buerstedde, J.-M. C1 - 3626 C2 - 22227 SP - 967-974 TI - Activation-induced cytidine deaminase initiates immunoglobulin gene conversion and hypermutation by a common intermediate. JO - PLoS Biol. VL - 2 IS - 7 PB - Public Library of Science PY - 2004 SN - 1544-9173 ER - TY - JOUR AB - The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology. AU - Imanishi, T.* AU - Itoh, T.* AU - Suzuki, Y.* AU - O'Donovan, C.* AU - Fukuchi, S.* AU - Koyanagi, K.O.* AU - Barrero, R.A.* AU - Tamura, T.* AU - Yamaguchi-Kabata, Y.* AU - Tanino, M.* AU - Yura, K.* AU - Miyazaki, S.* AU - Ikeo, K.* AU - Homma, K.* AU - Kasprzyk, A.* AU - Nishikawa, T.* AU - Hirakawa, M.* AU - Thierry-Mieg, J.* AU - Thierry-Mieg, D.* AU - Ashurst, J.* AU - Jia, L.* AU - Nakao, M.* AU - Thomas, M.A.* AU - Mulder, N.* AU - Karavidopoulou, Y.* AU - Jin, L.* AU - Kim, S.* AU - Yasuda, T.* AU - Lenhard, B.* AU - Eveno, E.* AU - Yamasaki, C.* AU - Takeda, J.* AU - Gough, C.* AU - Hilton, P.* AU - Fujii, Y.* AU - Sakai, H.* AU - Tanaka, S.* AU - Amid, C. AU - Bellgard, M.* AU - Bonaldo Mde, F.* AU - Bono, H.* AU - Bromberg, S.K.* AU - Brookes, A.J.* AU - Bruford, E.* AU - Carninci, P.* AU - Chelala, C.* AU - Couillault, C.* AU - de Souza, S.J.* AU - Debily, M.A.* AU - Devignes, M.D.* AU - Dubchak, I.* AU - Endo, T.* AU - Estreicher, A.* AU - Eyras, E.* AU - Fukami-Kobayashi, K.* AU - Gopinath, G.R.* AU - Graudens, E.* AU - Hahn, Y.* AU - Han, M. AU - Han, Z.G.* AU - Hanada, K.* AU - Hanaoka, H.* AU - Harada, E.* AU - Hashimoto, K.* AU - Hinz, U.* AU - Hirai, M.* AU - Hishiki, T.* AU - Hopkinson, I.* AU - Imbeaud, S.* AU - Inoko, H.* AU - Kanapin, A.* AU - Kaneko, Y.* AU - Kasukawa, T.* AU - Kelso, J.* AU - Kersey, P.* AU - Kikuno, R.* AU - Kimura, K.* AU - Korn, B.* AU - Kuryshev, V.* AU - Makalowska, I.* AU - Makino, T.* AU - Mano, S.* AU - Mariage-Samson, R.* AU - Mashima, J.* AU - Matsuda, H.* AU - Mewes, H.-W. AU - Minoshima, S.* AU - Nagai, K.* AU - Nagasaki, H.* AU - Nagata, N.* AU - Nigam, R.* AU - Ogasawara, O.* AU - Ohara, O.* AU - Ohtsubo, M.* AU - Okada, N.* AU - Okido, T.* AU - Oota, S.* AU - Ota, M.* AU - Ota, T.* AU - Otsuki, T.* AU - Piatier-Tonneau, D.* AU - Poustka, A.* AU - Ren, S.X.* AU - Saitou, N.* AU - Sakai, K.* AU - Sakamoto, S.* AU - Sakate, R.* AU - Schupp, I.* AU - Servant, F.* AU - Sherry, S.* AU - Shiba, R.* AU - Shimizu, N.* AU - Shimoyama, M.* AU - Simpson, A.J.* AU - Soares, B.* AU - Steward, C.* AU - Suwa, M.* AU - Suzuki, M.* AU - Takahashi, A.* AU - Tamiya, G.* AU - Tanaka, H.* AU - Taylor, T.* AU - Terwilliger, J.D.* AU - Unneberg, P.* AU - Veeramachaneni, V.* AU - Watanabe, S.* AU - Wilming, L.* AU - Yasuda, N.* AU - Yoo, H.S.* AU - Stodolsky, M.* AU - Makalowski, W.* AU - Go, M.* AU - Nakai, K.* AU - Takagi, T.* AU - Kanehisa, M.* AU - Sakaki, Y.* AU - Quackenbush, J.* AU - Okazaki, Y.* AU - Hayashizaki, Y.* AU - Hide, W.* AU - Chakraborty, R.* AU - Nishikawa, K.* AU - Sugawara, H.* AU - Tateno, Y.* AU - Chen, Z.* AU - Oishi, M.* AU - Tonellato, P.* AU - Apweiler, R.* AU - Okubo, K.* AU - Wagner, L.* AU - Wiemann, S.* AU - Strausberg, R.L.* AU - Isogai, T.* AU - Auffray, C.* AU - Nomura, N.* AU - Gojobori, T.* AU - Sugano, S.* C1 - 3424 C2 - 22385 SP - 856-875 TI - Integrative annotation of 21,037 human genetes validated by full-length cDNA clones. JO - PLoS Biol. VL - 2 IS - 6 PB - Public Library of Science PY - 2004 SN - 1544-9173 ER - TY - JOUR AB - The hallmark of Parkinson's disease (PD) is the selective loss of dopamine neurons in the ventral midbrain. Although the cause of neurodegeneration in PD is unknown, a Mendelian inheritance pattern is observed in rare cases, indicating a genetic factor. Furthermore, pathological analyses of PD substantia nigra have correlated cellular oxidative stress and altered proteasomal function with PD. Homozygous mutations in DJ-1 were recently described in two families with autosomal recessive Parkinsonism, one of which is a large deletion that is likely to lead to loss of function. Here we show that embryonic stem cells deficient in DJ-1 display increased sensitivity to oxidative stress and proteasomal inhibition. The accumulation of reactive oxygen species in toxin-treated DJ-1-deficient cells initially appears normal, but these cells are unable to cope with the consequent damage that ultimately leads to apoptotic death. Furthermore, we find that dopamine neurons derived from in vitro-differentiated DJ-1-deficient embryonic stem cells display decreased survival and increased sensitivity to oxidative stress. These data are consistent with a protective role for DJ-1, and demonstrate the utility of genetically modified embryonic stem cell-derived neurons as cellular models of neuronal disorders. AU - Martinat, C.* AU - Shendelman, S.* AU - Jonason, A.* AU - Leete, T.* AU - Beal, M.F.* AU - Yang, L.* AU - Floß, T. AU - Abeliovich, A.* C1 - 4287 C2 - 22411 SP - 1754-1763 TI - Sensitivity to oxidative stress in DJ-1-deficient dopamine neurons: An ES-derived cell model of primary parkinsonism. JO - PLoS Biol. VL - 2 IS - 11 PB - Public Library of Science PY - 2004 SN - 1544-9173 ER - TY - JOUR AB - In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans. AU - Prokisch, H. AU - Scharfe, C.* AU - Camp, D.G.* AU - Xiao, W.* AU - David, L.* AU - Andreoli, C. AU - Monroe, M.E.* AU - Moore, R.J.* AU - Gritsenko, M.A.* AU - Kozany, C. AU - Hixson, K.K.* AU - Mottaz, H.M.* AU - Zischka, H. AU - Ueffing, M. AU - Herman, Z.S.* AU - Davis, R.W.* AU - Meitinger, T. AU - Oefner, P.J.* AU - Smith, R.D.* AU - Steinmetz, L.M. C1 - 2270 C2 - 22471 SP - 795-804 TI - Integrative analysis of the mitochondrial proteome in yeast. JO - PLoS Biol. VL - 2 IS - 6 PB - Public Library of Science PY - 2004 SN - 1544-9173 ER -