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1.  Architecture of an RNA polymerase II transcription pre-initiation complex 
Science (New York, N.Y.)  2013;342(6159):1238724.
Summary
The protein density and arrangement of subunits of a complete, 31-protein, RNA polymerase II (pol II) transcription pre-initiation complex (PIC) were determined by cryo-electron microscopy and a combination of chemical cross-linking and mass spectrometry. The PIC showed a marked division in two parts, one containing all the general transcription factors (GTFs), and the other pol II. Promoter DNA was associated only with the GTFs, suspended above the pol II cleft and not in contact with pol II. This structural principle of the PIC underlies its conversion to a transcriptionally active state; the PIC is poised for the formation of a transcription bubble and descent of the DNA into the pol II cleft.
doi:10.1126/science.1238724
PMCID: PMC4039082  PMID: 24072820
2.  International Pediatric MS Study Group Clinical Trials Summit 
Neurology  2013;80(12):1161-1168.
Objective:
Pediatric studies for new biological agents are mandated by recent legislation, necessitating careful thought to evaluation of emerging multiple sclerosis (MS) therapies in children with MS. Challenges include a small patient population, the lack of prior randomized clinical trials, and ethical concerns. The goal of this meeting was to assess areas of consensus regarding clinical trial design and outcome measures among academic experts involved in pediatric MS care and research.
Methods:
The Steering Committee of the International Pediatric MS Study Group identified key focus areas for discussion. A total of 69 meeting attendees were assembled, including 35 academic experts. Regulatory and pharmaceutical representatives also attended, and provided input, which informed academic expert consensus decisions.
Results:
The academic experts agreed that clinical trials were necessary in pediatric MS to obtain pharmacokinetic, safety and efficacy data, and regulatory approval allowing for greater medication access. The academic experts agreed that relapse was an appropriate primary outcome measure for phase III pediatric trials. An international standardized cognitive battery was identified. The pros and cons of various trial designs were discussed. Guidelines surrounding MRI studies, pharmacokinetics, pharmacodynamics, and registries were developed. The academic experts agreed that given the limited subject pool, a stepwise approach to the launch of clinical trials for the most promising medications is necessary in order to ensure study completion. Alternative approaches could result in unethical exposure of patients to trial conditions without gaining knowledge.
Conclusion:
Consensus points for conduct of clinical trials in the rare disease pediatric MS were identified amongst a panel of academic experts, informed by regulatory and industry stakeholders.
doi:10.1212/WNL.0b013e318288694e
PMCID: PMC3662305  PMID: 23509048
3.  Dynamics of the Translational Machinery 
Current opinion in structural biology  2011;21(1):10.1016/j.sbi.2010.11.007.
The recent growth in single molecule studies of translation has provided an insight into the molecular mechanism of ribosomal function. Single molecule fluorescence approaches allowed direct observation of the structural rearrangements occurring during translation and revealed dynamic motions of the ribosome and its ligands. These studies demonstrated how ligand binding affects dynamics of the ribosome, and the role of the conformational sampling in large-scale rearrangements intrinsic to translation elongation. The application of time-resolved cryo-electron microscopy revealed new conformational intermediates during back-translocation providing an insight into ribosomal dynamics from an alternative perspective. Recent developments permitted examination of conformational and compositional dynamics of the ribosome in real-time through multiple cycles of elongation at the single molecule level. The zero-mode waveguide approach allowed direct observation of the compositional dynamics of tRNA occupancy on the elongating ribosome. The emergence of single molecule in vivo techniques provided insights into the mechanism and regulation of translation at the organismal level.
doi:10.1016/j.sbi.2010.11.007
PMCID: PMC3826783  PMID: 21256733
4.  Microarray Comparison of Anterior and Posterior Drosophila Wing Imaginal Disc Cells Identifies Novel Wing Genes 
G3: Genes|Genomes|Genetics  2013;3(8):1353-1362.
Signaling between cells in the anterior (A) and posterior (P) compartments directs Drosophila wing disc development and is dependent on expression of the homeodomain transcription factor Engrailed (En) in P cells. Downstream of en, posteriorly expressed Hedgehog (Hh) protein signals across the A/P border to establish a developmental organizer that directs pattern formation and growth throughout the wing primordium. Here we extend investigations of the processes downstream of en by using expression array analysis to compare A and P cells. A total of 102 candidate genes were identified that express differentially in the A and P compartments; four were characterized: Stubble (Sb) expression is restricted to A cells due to repression by en. CG15905, CG16884; CG10200/hase und igel (hui) are expressed in A cells downstream of Hh signaling; and RNA interference for hui, Stubble, and CG16884 revealed that each is essential to wing development.
doi:10.1534/g3.113.006569
PMCID: PMC3737175  PMID: 23749451
anteroposterior compartment border; pattern formation; expression microarray; engrailed; hedgehog
5.  Smoothened Regulates Activator and Repressor Functions of Hedgehog Signaling via Two Distinct Mechanisms* 
The Journal of biological chemistry  2006;281(11):7237-7243.
The secreted protein Hedgehog (Hh) plays an important role in metazoan development and as a survival factor for many human tumors. In both cases, Hh signaling proceeds through the activation of the seven-transmembrane protein Smoothened (Smo), which is thought to convert the Gli family of transcription factors from transcriptional repressors to transcriptional activators. Here, we provide evidence that Smo signals to the Hh signaling complex, which consists of the kinesin-related protein Costal2 (Cos2), the protein kinase Fused (Fu), and the Drosophila Gli homolog cubitus interruptus (Ci), in two distinct manners. We show that many of the commonly observed molecular events following Hh signaling are not transmitted in a linear fashion but instead are activated through two signals that bifurcate at Smo to independently affect activator and repressor pools of Ci.
doi:10.1074/jbc.M510169200
PMCID: PMC3677211  PMID: 16423832
6.  An Essential Role for Zygotic Expression in the Pre-Cellular Drosophila Embryo 
PLoS Genetics  2013;9(4):e1003428.
The Drosophila embryo proceeds through thirteen mitotic divisions as a syncytium. Its nuclei distribute in the embryo's interior during the first six divisions, dividing synchronously with a cycle time of less than ten minutes. After seven divisions (nuclear cycle 8), the syncytial blastoderm forms as the nuclei approach the embryo surface and slow their cycle time; subsequent divisions proceed in waves that initiate at the poles. Because genetic studies have not identified zygotic mutants that affect the early divisions and because transcription has not been detected before cycle 8, the early, pre-blastoderm embryo has been considered to rely entirely on maternal contributions and to be transcriptionally silent. Our studies identified several abnormal phenotypes in live engrailed (en) mutant embryos prior to cycle 8, as well as a small group of genes that are transcribed in embryos prior to cycle 7. Nuclei in en embryos divide asynchronously, an abnormality that was detected as early as nuclear cycle 2–3. Anti-En antibody detected nuclear En protein in embryos at cycle 2, and expression of an En:GFP fusion protein encoded in the paternal genome was also detected in cycle 2 nuclei. These findings demonstrate that the Drosophila embryo is functionally competent for gene expression prior to the onset of its rapid nuclear divisions and that the embryo requires functions that are expressed in the zygote in order to faithfully prosecute its early, pre-cellularization mitotic cycles.
Author Summary
Genetic studies identified many genes that are required during Drosophila oogenesis to endow the embryo with structures and components it will need to develop; they have also identified many genes that the embryo must express. However, measures of transcription have detected zygotic transcripts only after seven nuclear divisions, and many studies have concluded that zygotic mutants do not affect embryos prior to cellularization. The model that has emerged is that the earliest stages of embryogenesis rely solely on maternal stores and do not receive input from the zygotic genome. The fact that the embryo's nuclei divide rapidly with a cycling time of less than ten minutes has been interpreted to support this model, because it has been assumed that the nuclear cycle is too short for productive gene expression. Using sensitive measures of transcription and histological procedures that detect subtle differences, we found evidence for expression as early as nuclear cycle 2, and we identified a requirement for zygotic gene expression in embryos with just 2–4 nuclei. These findings challenge the idea that the Drosophila embryo is entirely pre-programmed and that its early development is under exclusive maternal control.
doi:10.1371/journal.pgen.1003428
PMCID: PMC3616919  PMID: 23593026
7.  Pentoxifylline as a rescue treatment for DMD 
Neurology  2012;78(12):904-913.
Objective:
To determine whether pentoxifylline (PTX) slows the decline of muscle strength and function in ambulatory boys with Duchenne muscular dystrophy (DMD).
Methods:
This was a multicenter, randomized, double-blinded, controlled trial comparing 12 months of daily treatment with PTX or placebo in corticosteroid-treated boys with DMD using a slow-release PTX formulation (∼20 mg/kg/day). The primary outcome was the change in mean total quantitative muscle testing (QMT) score. Secondary outcomes included changes in QMT subscales, manual muscle strength, pulmonary function, and timed function tests. Outcomes were compared using Student t tests and a linear mixed-effects model. Adverse events (AEs) were compared using the Fisher exact test.
Results:
A total of 64 boys with DMD with a mean age of 9.9 ± 2.9 years were randomly assigned to PTX or placebo in 11 participating Cooperative International Neuromuscular Research Group centers. There was no significant difference between PTX and the placebo group in total QMT scores (p = 0.14) or in most of the secondary outcomes after a 12-month treatment. The use of PTX was associated with mild to moderate gastrointestinal or hematologic AEs.
Conclusion:
The addition of PTX to corticosteroid-treated boys with DMD at a moderate to late ambulatory stage of disease did not improve or halt the deterioration of muscle strength and function over a 12-month study period.
Classification of evidence:
This study provides Class I evidence that treatment with PTX does not prevent deterioration in muscle function or strength in corticosteroid-treated boys with DMD.
doi:10.1212/WNL.0b013e31824c46be
PMCID: PMC3306159  PMID: 22402864
8.  Familial Cortical Myoclonus with a Mutation in NOL3 
Annals of neurology  2012;72(2):175-183.
Objective
Myoclonus is characterized by sudden, brief involuntary movements and its presence is debilitating. We identified a family suffering from adult-onset, cortical myoclonus without associated seizures. We performed clinical, electrophysiological, and genetic studies to define this phenotype.
Methods
A large, four-generation family with history of myoclonus underwent careful questioning, examination, and electrophysiological testing. Thirty-five family members donated blood samples for genetic analysis, which included SNP mapping, microsatellite linkage, targeted massively parallel sequencing, and Sanger sequencing. In silico and in vitro experiments were performed to investigate functional significance of the mutation.
Results
We identified 11 members of a Canadian Mennonite family suffering from adult-onset, slowly progressive, disabling, multifocal myoclonus. Somatosensory evoked potentials indicated a cortical origin of the myoclonus. There were no associated seizures. Some severely affected individuals developed signs of progressive cerebellar ataxia of variable severity late in the course of their illness. The phenotype was inherited in an autosomal dominant fashion. We demonstrated linkage to chromosome 16q21-22.1. We then sequenced all coding sequence in the critical region, identifying only a single co-segregating, novel, nonsynonymous mutation, which resides in the gene NOL3. Furthermore, this mutation was found to alter post-translational modification of NOL3 protein in vitro.
Interpretation
We propose that Familial Cortical Myoclonus (FCM) is a novel movement disorder that may be caused by mutation in NOL3. Further investigation of the role of NOL3 in neuronal physiology may shed light on neuronal membrane hyperexcitability and pathophysiology of myoclonus and related disorders.
doi:10.1002/ana.23666
PMCID: PMC3431191  PMID: 22926851
9.  Extended Postinterventional Tumor Necrosis—Implication for Outcome in Liver Transplant Patients with Advanced HCC 
PLoS ONE  2013;8(1):e53960.
Background
Locoregional interventional bridging therapy (IBT) is an accepted neoadjuvant approach in liver transplant candidates with hepatocellular carcinoma (HCC). However, the prognostic value of IBT in patients with advanced HCC is still undefined.
Aim
The aim of this trial was to evaluate the impact of postinterventional tumor necrosis on recurrence-free long-term survival after liver transplantation (LT) in patients with HCC, especially focusing on those exceeding the Milan criteria on pretransplant radiographic imaging.
Patients and Methods
A total of 93 consecutive liver transplant candidates with HCC were included in this trial. In 36 patients, tumors were clinically staged beyond Milan criteria prior LT. Fifty-nine patients underwent IBT by transarterial chemoembolization or radiofrequency ablation pretransplantation. Postinterventional tumor necrosis rate as assessed at liver explant pathology was correlated with outcome post-LT.
Results
There was no significant difference in 5-year tumor-free survival rate between the IBT- and the non-IBT subpopulation (78% versus 68%, P = 0.25). However, tumor response following IBT (≥50% tumor necrosis rate at explant pathology) resulted in a significantly better outcome 5 years post-LT (96%) than tumor non-response to IBT (<50% tumor necrosis rate at explant pathology; 21%; P<0.001). Five-year recurrence-free survival rate was 80% in Milan Out patients with extended post-IBT tumor necrosis versus 0% in Milan Out patients without tumor response to IBT (P<0.001). None of macromorphological HCC features, but only the absence of increased 18F-fluoro-deoxy-glucose (18FDG) uptake on pretransplant positron emission tomography (PET) was identified as independent predictor of postinterventional tumor response (P<0.001).
Conclusion
Our results implicate that extended postinterventional tumor necrosis promotes recurrence-free long-term survival in patients with HCC beyond standard criteria. Pretransplant PET assessment may identify those patients with advanced HCC that will benefit from post-IBT tumor response and may, thereby, achieve excellent posttransplant outcome.
doi:10.1371/journal.pone.0053960
PMCID: PMC3551930  PMID: 23349774
10.  Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration 
Nature genetics  2012;44(6):704-708.
RNA exosomes are multi-subunit complexes conserved throughout evolution1 and emerging as the major cellular machinery for processing, surveillance, and turnover of a diverse spectrum of coding and non-coding RNA substrates essential for viability2. By exome sequencing, we discovered recessive mutations in exosome component 3 (EXOSC3) in four siblings with infantile spinal motor neuron disease, cerebellar atrophy, progressive microcephaly, and profound global developmental delay, consistent with pontocerebellar hypoplasia type 1 [PCH1; OMIM 607596]3–6. We identified mutations in EXOSC3 in an additional 8 of 12 families with PCH1. Morpholino knockdown of exosc3 in zebrafish embryos caused embryonic maldevelopment with small brain and poor motility, reminiscent of human clinical features and largely rescued by coinjected wildtype but not mutant exosc3 mRNA. These findings represent the first example of an RNA exosome gene responsible for a human disease and further implicate dysregulation of RNA processing in cerebellar and spinal motor neuron maldevelopment and degeneration.
doi:10.1038/ng.2254
PMCID: PMC3366034  PMID: 22544365
11.  Niche-modulated and niche-modulating genes in bone marrow cells 
Blood Cancer Journal  2012;2(12):e97-.
Bone marrow (BM) cells depend on their niche for growth and survival. However, the genes modulated by niche stimuli have not been discriminated yet. For this purpose, we investigated BM aspirations from patients with various hematological malignancies. Each aspirate was fractionated, and the various samples were fixed at different time points and analyzed by microarray. Identification of niche-modulated genes relied on sustained change in expression following loss of niche regulation. Compared with the reference (‘authentic') samples, which were fixed immediately following aspiration, the BM samples fixed after longer stay out-of-niche acquired numerous changes in gene-expression profile (GEP). The overall genes modulated included a common subset of functionally diverse genes displaying prompt and sustained ‘switch' in expression irrespective of the tumor type. Interestingly, the ‘switch' in GEP was reversible and turned ‘off-and-on' again in culture conditions, resuming cell–cell–matrix contact versus respread into suspension, respectively. Moreover, the resuming of contact prolonged the survival of tumor cells out-of-niche, and the regression of the ‘contactless switch' was followed by induction of a new set of genes, this time mainly encoding extracellular proteins including angiogenic factors and extracellular matrix proteins. Our data set, being unique in authentic expression design, uncovered niche-modulated and niche-modulating genes capable of controlling homing, expansion and angiogenesis.
doi:10.1038/bcj.2012.42
PMCID: PMC3542477  PMID: 23241658
gene-expression profile; myeloma; leukemia; contactless gene signature; niche-modulated genes; niche-modulating genes
13.  Randomized, blinded trial of weekend vs daily prednisone in Duchenne muscular dystrophy 
Neurology  2011;77(5):444-452.
Objective:
To perform a double-blind, randomized study comparing efficacy and safety of daily and weekend prednisone in boys with Duchenne muscular dystrophy (DMD).
Methods:
A total of 64 boys with DMD who were between 4 and 10 years of age were randomized at 1 of 12 centers of the Cooperative International Neuromuscular Research Group. Efficacy and safety of 2 prednisone schedules (daily 0.75 mg/kg/day and weekend 10 mg/kg/wk) were evaluated over 12 months.
Results:
Equivalence was met for weekend and daily dosing of prednisone for the primary outcomes of quantitative muscle testing (QMT) arm score and QMT leg score. Secondary strength scores for QMT elbow flexors also showed equivalence between the 2 treatment groups. Overall side effect profiles of height and weight, bone density, cataract formation, blood pressure, and behavior, analyzed at 12 months, did not differ between weekend and daily dosing of prednisone.
Conclusions:
Weekend dosing of prednisone is equally beneficial to the standard daily dosing of prednisone. Analysis of side effect profiles demonstrated overall tolerability of both dosing regimens.
Classification of evidence:
This study provides Class I evidence that weekend prednisone dosing is as safe and effective as daily prednisone in preserving muscle strength and preventing body mass index increases in boys with DMD over a 12-month period.
doi:10.1212/WNL.0b013e318227b164
PMCID: PMC3146308  PMID: 21753160
14.  Cytoneme-Mediated Delivery of Hedgehog Regulates the Expression of Bone Morphogenetic Proteins to Maintain Germline Stem Cells in Drosophila 
PLoS Biology  2012;10(4):e1001298.
Genetic manipulation of the germline stem cell niche in Drosophila ovaries reveals that support cells ensure the maintenance of stem cells by modulating the spread of Hedgehog within the niche.
Stem cells reside in specialised microenvironments, or niches, which often contain support cells that control stem cell maintenance and proliferation. Hedgehog (Hh) proteins mediate homeostasis in several adult niches, but a detailed understanding of Hh signalling in stem cell regulation is lacking. Studying the Drosophila female germline stem cell (GSC) niche, we show that Hh acts as a critical juxtacrine signal to maintain the normal GSC population of the ovary. Hh production in cap cells, a type of niche support cells, is regulated by the Engrailed transcription factor. Hh is then secreted to a second, adjacent population of niche cells, the escort cells, where it activates transcription of the GSC essential factors Decapentaplegic (Dpp) and Glass bottom boat (Gbb). In wild-type niches, Hh protein decorates short filopodia that originate in the support cap cells and that are functionally relevant, as they are required to transduce the Hh pathway in the escort cells and to maintain a normal population of GSCs. These filopodia, reminiscent of wing disc cytonemes, grow several fold in length if Hh signalling is impaired within the niche. Because these long cytonemes project directionally towards the signalling-deficient region, cap cells sense and react to the strength of Hh pathway transduction in the niche. Thus, the GSC niche responds to insufficient Hh signalling by increasing the range of Hh spreading. Although the signal(s) perceived by the cap cells and the receptor(s) involved are still unknown, our results emphasise the integration of signals necessary to maintain a functional niche and the plasticity of cellular niches to respond to challenging physiological conditions.
Author Summary
The Drosophila ovary contains a well-defined stem cell niche that hosts 2–3 germline stem cells (GSCs). The Hedgehog (Hh) family of signalling proteins mediates cellular homeostasis in several adult tissues, and here we decipher the detailed mechanism of action of Hh in the adult female GSC niche. We demonstrate that Hh acts in a juxtacrine manner (i.e., it requires physical contact between the cells involved) to maintain the normal pool of GSCs in the ovarian niche. Hh is produced in one type of niche support cell (the cap cells), and it is received, upon secretion, by a second, neighbouring population of niche cells (the escort cells). In the latter, we show that the Hh signalling pathway regulates the expression of the Drosophila Bone Morphogenetic Protein (BMP) homologues and essential stem cell factors decapentaplegic (dpp) and glass bottom boat (gbb). We also find that Hh distribution in the GSC niche is mediated by short cellular projections, reminiscent of wing disc cytonemes, although they grow from the (Hh) signal-producing cells towards the receiving cells. Under conditions of low levels of Hh protein and/or Hh signalling within the niche, cap cells emit up to 6-fold longer Hh-decorated cytonemes towards the signalling-deficient area of the niche. Our data reveal that stem cell niches are dynamic structures that can sense, and react to, changes in the activity of essential stem cell factors to prevent stem cell differentiation.
doi:10.1371/journal.pbio.1001298
PMCID: PMC3317903  PMID: 22509132
15.  Expression and Characterization of Drosophila Signal Peptide Peptidase-Like (sppL), a Gene That Encodes an Intramembrane Protease 
PLoS ONE  2012;7(3):e33827.
Intramembrane proteases of the Signal Peptide Peptidase (SPP) family play important roles in developmental, metabolic and signaling pathways. Although vertebrates have one SPP and four SPP-like (SPPL) genes, we found that insect genomes encode one Spp and one SppL. Characterization of the Drosophila sppL gene revealed that the predicted SppL protein is a highly conserved structural homolog of the vertebrate SPPL3 proteases, with a predicted nine-transmembrane topology, an active site containing aspartyl residues within a transmembrane region, and a carboxy-terminal PAL domain. SppL protein localized to both the Golgi and ER. Whereas spp is an essential gene that is required during early larval stages and whereas spp loss-of-function reduced the unfolded protein response (UPR), sppL loss of function had no apparent phenotype. This was unexpected given that genetic knockdown phenotypes in other organisms suggested significant roles for Spp-related proteases.
doi:10.1371/journal.pone.0033827
PMCID: PMC3306293  PMID: 22439002
16.  Selective Removal of Promoter Nucleosomes by the RSC Chromatin Remodeling Complex 
Summary
Purified chromatin rings, excised from the PHO5 locus of yeast in transcriptionally repressed and activated states, were remodeled with RSC and ATP. Nucleosomes were translocated, and those originating on the promoter of repressed rings were removed, whereas those originating on the open reading frame (ORF) were retained. Treatment of the repressed rings with histone deacetylase diminished the removal of promoter nucleosomes. These findings point to a principle of promoter chromatin remodeling for transcription, that promoter-specificity resides primarily in the nucleosomes, rather than in the remodeling complex that acts upon them.
doi:10.1038/nsmb.2072
PMCID: PMC3150231  PMID: 21725295
17.  Initiation Complex Structure and Promoter Proofreading 
Science (New York, N.Y.)  2011;333(6042):633-637.
doi:10.1126/science.1206629
PMCID: PMC3179255  PMID: 21798951
18.  Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics* 
High density tiling arrays are an effective strategy for genome-wide identification of transcription factor binding regions. Sliding window methods that calculate moving averages of log ratios or t-statistics have been useful for the analysis of tiling array data. Here, we present a method that generalizes the moving average approach to evaluate sliding windows of p-values by using combined p-value statistics. In particular, the combined p-value framework can be useful in situations when taking averages of the corresponding test-statistic for the hypothesis may not be appropriate or when it is difficult to assess the significance of these averages. We exhibit the strengths of the combined p-values methods on Drosophila tiling array data and assess their ability to predict genomic regions enriched for transcription factor binding. The predictions are evaluated based on their proximity to target genes and their enrichment of known transcription factor binding sites. We also present an application for the generalization of the moving average based on integrating two different tiling array experiments.
doi:10.2202/1544-6115.1434
PMCID: PMC2942027  PMID: 20812907
transcription factor; binding sequence; tiling array; combined p-value
19.  Synthesis and Bioconjugation of 2 and 3 nm-diameter Gold Nanoparticles 
Bioconjugate chemistry  2010;21(2):214-218.
By adjustment of solvent conditions for synthesis, virtually monodisperse 4-mercaptobenzoic acid (p-MBA) monolayer-protected gold nanoparticles, 2 and 3 nm in diameter were obtained. Large single crystals of the 2 nm particles could be grown from the reaction mixture. Uniformity was also demonstrated by the formation of two-dimensional arrays and by quantitative high-angle annular dark-field scanning transmission electron microscopy. The 2 and 3 nm particles were spontaneously reactive for conjugation with proteins and DNA, and further reaction could be prevented by repassivation with glutathione. Conjugates with antibody Fc fragment could be used to identify TAP-tagged proteins of interest in electron micrographs, through the binding of a pair of particles to the pair of protein A domains in the TAP tag.
doi:10.1021/bc900135d
PMCID: PMC3113727  PMID: 20099843
20.  Specificity of Drosophila Cytonemes for Distinct Signaling Pathways 
Science (New York, N.Y.)  2011;332(6027):354-358.
Cytonemes are types of filopodia in the Drosophila wing imaginal disc that are proposed to serve as conduits in which morphogen signaling proteins move between producing and target cells. We investigated the specificity of cytonemes that are made by target cells. Cells in wing discs made cytonemes that responded specifically to Decapentaplegic (Dpp) and cells in eye discs made cytonemes that responded specifically to Spitz (the Drosophila epidermal growth factor protein). Tracheal cells had at least two types: one made in response to Branchless (a Drosophila fibroblast growth factor protein, Bnl), to which they segregate the Bnl receptor, and another to which they segregate the Dpp receptor. We conclude that cells can make several types of cytonemes, each of which responds specifically to a signaling pathway by means of the selective presence of a particular signaling protein receptor that has been localized to that cytoneme.
doi:10.1126/science.1198949
PMCID: PMC3109072  PMID: 21493861
21.  GAPDH Mediates Nitrosylation of Nuclear Proteins 
Nature cell biology  2010;12(11):1094-1100.
S-nitrosylation by nitric oxide (NO) is a major mode of signaling to cellular proteins1, including prominent nuclear proteins such as HDAC22 and PARP13. The high reactivity of the NO group with protein thiols implies the existence of selective targeting mechanisms. Specificity of NO signaling is often achieved by the binding of NO synthase (NOS) to target proteins, either directly4 or through scaffolding proteins such as PSD-955 and CAPON6. As the three principal isoforms of NOS - neuronal NOS (nNOS), endothelial NOS (eNOS), and inducible NOS (iNOS) - are primarily non-nuclear, the mechanisms by which nuclear proteins are selectively nitrosylated have been elusive. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is physiologically nitrosylated at its Cys150 residue, conferring upon it the ability to bind to Siah1, which possesses a nuclear localization signal and conveys nitrosylated GAPDH (SNO-GAPDH) to the nucleus7. We now show that SNO-GAPDH physiologically transnitrosylates nuclear proteins, including the deacetylating enzyme SIRT1, histone deacetylase-2 (HDAC2), and DNA-activated protein kinase (DNA-PK). Our findings reveal a novel mechanism for targeted nitrosylation of nuclear proteins and suggest that protein-protein transfer of NO groups may be a general mechanism in cellular signal transduction.
doi:10.1038/ncb2114
PMCID: PMC2972384  PMID: 20972425
22.  Anatomic Site Based Ploidy Analysis of Oral Premalignant Lesions 
Head and Neck Pathology  2009;4(1):10-14.
The location of oral leukoplakia correlates strongly with the probability of finding dysplastic or malignant alterations at biopsy. It is well established that early detection can dramatically improve the 5-year survival rates for oral squamous cell carcinomas. Since aneuploidy is predictive of future conversion to malignancy, we hypothesized that dysplastic lesions from high-risk sites (floor of mouth, tongue and lips) would exhibit greater aneuploidy than low-risk sites (palate, gingiva and buccal mucosa). Epithelial sections from 60 archival samples diagnosed as mild dysplasia (36 females, 20 males) from various high/low risk locations were stained with Blue Feulgen Stain for DNA Ploidy Analysis (Clarient, Aliso Viejo, CA) and ploidy was analyzed using a ChromaVision ACIS II (Clarient, ALiso Viejo, CA) Image cytometry system. A DNA histogram was generated using an image analyzing software that evaluated the amount of Feulgen stain which is proportional to the amount of nuclear DNA. An ANOVA analysis followed by the Student’s‘t’ test revealed significant differences between means (P ≤ 0.05). Lesions originating from lateral/ventral tongue (85%), floor of mouth (50%) and soft palate (44%) exhibited a higher frequency of aneuploidy than lesions from gingiva (22%) and lower lip (25%). This pilot study demonstrates that dysplastic lesions from high-risk sites such as the floor of the mouth and lateral/ventral tongue have higher frequency of aneuploidy.
doi:10.1007/s12105-009-0151-0
PMCID: PMC2825532  PMID: 20237983
Ploidy; Aneuploid; Oral leukoplakia; Dysplasia
23.  Regulation of Drosophila matrix metalloprotease Mmp2 is essential for wing imaginal disc:trachea association and air sac tubulogenesis 
Developmental biology  2009;335(2):317-326.
The Drosophila dorsal Air Sac Primordium (ASP) is a tracheal tube that grows toward Branchless FGF-expressing cells in the wing imaginal disc. We show that the ASP arises from a tracheal branch that invades the basal lamina of the disc to juxtapose directly with disc cells. We examined the role of matrix metalloproteases (Mmps), and found that reducing Mmp2 activity perturbed disc-trachea association, altered peritracheal distributions of Collagen IV and Perlecan, misregulated ASP growth, and abrogated development of the dorsal air sacs. Whereas the function of the membrane-tethered Mmp2 in the ASP is non-cell autonomous we find that it may have distinct tissue-specific roles in the ASP and disc. These findings demonstrate a critical role for Mmp2 in tubulogenesis post-induction, and implicate Mmp2 in regulating dynamic and essential changes to the extracellular matrix.
doi:10.1016/j.ydbio.2009.09.005
PMCID: PMC2784283  PMID: 19751719
Drosophila air sacs; tracheal morphogenesis; FGF; basal lamina; matrix metalloproteinase
24.  An Rtt109-Independent Role for Vps75 in Transcription-Associated Nucleosome Dynamics▿ †  
Molecular and Cellular Biology  2009;29(15):4220-4234.
The histone chaperone Vps75 forms a complex with, and stimulates the activity of, the histone acetyltransferase Rtt109. However, Vps75 can also be isolated on its own and might therefore possess Rtt109-independent functions. Analysis of epistatic miniarray profiles showed that VPS75 genetically interacts with factors involved in transcription regulation whereas RTT109 clusters with genes linked to DNA replication/repair. Additional genetic and biochemical experiments revealed a close relationship between Vps75 and RNA polymerase II. Furthermore, Vps75 is recruited to activated genes in an Rtt109-independent manner, and its genome-wide association with genes correlates with transcription rate. Expression microarray analysis identified a number of genes whose normal expression depends on VPS75. Interestingly, histone H2B dynamics at some of these genes are consistent with a role for Vps75 in histone H2A/H2B eviction/deposition during transcription. Indeed, reconstitution of nucleosome disassembly using the ATP-dependent chromatin remodeler Rsc and Vps75 revealed that these proteins can cooperate to remove H2A/H2B dimers from nucleosomes. These results indicate a role for Vps75 in nucleosome dynamics during transcription, and importantly, this function appears to be largely independent of Rtt109.
doi:10.1128/MCB.01882-08
PMCID: PMC2715805  PMID: 19470761
25.  Structure of an RNA Polymerase II–TFIIB Complex and the Transcription Initiation Mechanism 
Science (New York, N.Y.)  2009;327(5962):206.
Previous X-ray crystal structures have given insight into the mechanism of transcription and the role of general transcription factors in the initiation of the process. A previous structure at 4.5 Å resolution of an RNA polymerase II–general transcription factor TFIIB complex revealed the N-terminal region of TFIIB, including a loop termed the “B-finger” reaching into the active center of the polymerase where it may interact with both DNA and RNA, but this structure showed little of the C-terminal region. A new crystal structure of the same complex at 3.8 Å resolution obtained under different solution conditions is complementary with the previous one, revealing the C-terminal region of TFIIB, located above the polymerase active center cleft, but showing none of the B-finger. In the new structure, the linker between the N- and C-terminal regions can also be seen, snaking down from above the cleft towards the active center. The two structures, taken together with others previously obtained, dispel longstanding mysteries of the transcription initiation process.
doi:10.1126/science.1182015
PMCID: PMC2813267  PMID: 19965383

Results 1-25 (84)