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Find video protocols related to scientific articles indexed in Pubmed.
Use of a customized 3D "basket" to create a solitary split-thickness cranial graft from numerous split fragments in an infant.
J Neurosurg Pediatr
PUBLISHED: 06-20-2014
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While autologous split calvaria remains the preferred material for use in pediatric cranioplasty, it may be difficult to split the bone neatly into two distinct pieces, especially in infants and young children. In this paper, the authors present a technique in which numerous split pieces of bone can be readily joined together and conformed to the shape of the specific defect using a customized template and 3D trellis-like basket.
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How to get in and out of the skull: from tumi to "hammer and chisel" to the Gigli saw and the osteoplastic flap.
Neurosurg Focus
PUBLISHED: 04-09-2014
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Making "holes in the skull" is an ancient art and by some is considered the second oldest profession in the world-the first being prostitution. Early surgeons, and later on neurosurgeons, devised a number of ingenious ways to make a hole in the skull or elevate a depressed skull fracture. Trephined skulls from antiquity have now been found in most parts of world, showing that the art of trephining is not only ancient but clearly widespread. Beginning with antiquity the author traces the development of this surgical skill by reviewing the various tools used and surgical designs to perform what is now called a craniotomy.
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The Reverend Russell H. Conwell, W. Wayne Babcock, and the "soup bone" cranioplasties of 1915.
Neurosurg Focus
PUBLISHED: 04-02-2014
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In 1915, faced with 2 patients with large skull defects, W. Wayne Babcock, an obstetrician-gynecologist-turned-general surgeon, operating in a modest North Philadelphia hospital, did something extraordinary: he went to the hospital kitchen to look for a cranial graft. Based heavily on archival and other primary sources, the authors tell the remarkable tale of the "soup bone" cranioplasties of the Samaritan Hospital and place these operations within the context of the early modern American hospital.
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Five-year safety evaluation of maraviroc in HIV-1-infected treatment-experienced patients.
J. Acquir. Immune Defic. Syndr.
PUBLISHED: 01-15-2014
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Maraviroc is unique among approved antiretroviral drugs in targeting the host-cell chemokine coreceptor type-5 receptor. With its novel mechanism of action, we sought to describe the 5-year safety profile of maraviroc.
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Single molecule studies of RNA polymerase II transcription in vitro.
Transcription
PUBLISHED: 01-11-2014
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Eukaryotic mRNA transcription by RNA polymerase II (RNAP II) is the first step in gene expression and a key determinant of cellular regulation. Elucidating the mechanism by which RNAP II synthesizes RNA is therefore vital to determining how genes are controlled under diverse biological conditions. Significant advances in understanding RNAP II transcription have been achieved using classical biochemical and structural techniques; however, aspects of the transcription mechanism cannot be assessed using these approaches. The application of single-molecule techniques to study RNAP II transcription has provided new insight only obtainable by studying molecules in this complex system one at a time.
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Selection and characterization of a DNA aptamer that can discriminate between cJun/cJun and cJun/cFos.
PLoS ONE
PUBLISHED: 01-01-2014
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The AP-1 family of transcriptional activators plays pivotal roles in regulating a wide range of biological processes from the immune response to tumorigenesis. Determining the roles of specific AP-1 dimers in cells, however, has remained challenging because common molecular biology techniques are unable to distinguish between the role of, for example, cJun/cJun homodimers versus cJun/cFos heterodimers. Here we used SELEX (systematic evolution of ligands by exponential enrichment) to identify and characterize DNA aptamers that are >100-fold more specific for binding cJun/cJun compared to cJun/cFos, setting the foundation to investigate the biological functions of different AP-1 dimer compositions.
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Genotypic analysis of the V3 region of HIV from virologic nonresponders to maraviroc-containing regimens reveals distinct patterns of failure.
Antimicrob. Agents Chemother.
PUBLISHED: 09-30-2013
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Changes in HIV tropism from R5 to non-R5 or development of drug resistance is often associated with virologic failure in patients treated with maraviroc, a CCR5 antagonist. We sought to examine changes in HIV envelope sequences and inferred tropism in patients who did not respond to maraviroc-based regimens. We selected 181 patients who experienced early virologic failure on maraviroc-containing therapy in the MOTIVATE trials. All patients had R5 HIV by the original Trofile assay before entry. We used population-based sequencing methods and the geno2pheno algorithm to examine changes in tropism and V3 sequences at the time of failure. Using deep sequencing, we assessed whether V3 sequences observed at failure emerged from preexisting subpopulations. From population genotyping data at failure, 90 patients had R5 results, and 91 had non-R5 results. Of the latter group, the geno2pheno false-positive rate (FPR) value fell from a median of 20 at screening to 1.1 at failure. By deep sequencing, the median percentage of non-R5 variants in these patients rose from 1.4% to 99.5% after a median of 4 weeks on maraviroc. In 70% of cases, deep sequencing could detect a pretreatment CXCR4-using subpopulation, which emerged at failure. Overall, there were two distinct patterns of failure of maraviroc. Patients failing with R5 generally had few V3 substitutions and low non-R5 prevalence by deep sequencing. Patients with non-R5 HIV who were failing developed very-high-prevalence non-R5 HIV (median, 99%) and had very low geno2pheno values.
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Successful treatment of post-shunt craniocerebral disproportion by coupling gradual external cranial vault distraction with continuous intracranial pressure monitoring.
J Neurosurg Pediatr
PUBLISHED: 03-29-2013
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A subset of hydrocephalic patients in whom shunts are placed at an early age will develop craniocerebral disproportion (CCD), an iatrogenic mismatch between the fixed intracranial volume and the growing brain. The lack of a reliable, reproducible method to diagnose this condition, however, has hampered attempts to treat it appropriately. For those practitioners who acknowledge the need to create more intracranial space in these patients, the lack of agreed-upon therapeutic end points for cranial vault expansion has limited the use of such techniques and has sometimes led to problems of underexpansion. Here, the authors present a definition of CCD based primarily on the temporal correlation of plateau waves on intracranial pressure (ICP) monitoring and headache exacerbation. The authors describe a technique of exploiting continued ICP monitoring during progressive cranial expansion in which the goal of distraction is the cessation of plateau waves. Previously encountered problems of underexpansion may be mitigated through the simultaneous use of ICP monitors and gradual cranial expansion over time.
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NFATc2 recruits cJun homodimers to an NFAT site to synergistically activate interleukin-2 transcription.
Mol. Immunol.
PUBLISHED: 03-26-2013
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Transcription of interleukin-2 (IL-2), a pivotal cytokine in the mammalian immune response, is induced by NFAT and AP-1 transcriptional activators in stimulated T cells. NFATc2 and cJun drive high levels of synergistic human IL-2 transcription, which requires a unique interaction between the C-terminal activation domain of NFATc2 and cJun homodimers. Here we studied the mechanism by which this interaction contributes to synergistic activation of IL-2 transcription. We found that NFATc2 can recruit cJun homodimers to the -45 NFAT element, which lacks a neighboring AP-1 site. The bZip domain of cJun is sufficient to interact with the C-terminal activation domain of NFATc2 in the absence of DNA and this interaction is inhibited by AP-1 DNA. When the -45 NFAT site was replaced by either an NFAT/AP-1 composite site or a single AP-1 site the specificity for cJun homodimers in synergistically activating IL-2 transcription was lost, and cJun/cFos heterodimers strongly activated transcription. These studies support a model in which IL-2 transcriptional synergy is mediated by the unique recruitment of a cJun homodimer to the -45 NFAT site by NFATc2, where it acts as a co-activator for IL-2 transcription.
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Using FRET to monitor protein-induced DNA bending: the TBP-TATA complex as a model system.
Methods Mol. Biol.
PUBLISHED: 02-26-2013
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Proteins that bind to DNA can elicit changes in DNA conformation, such as bending and looping, which are important signals for later events such as transcription. TATA-binding protein (TBP) is one example of a protein that elicits a conformational change in DNA; TBP binds and sharply bends its recognition sequence, which is thought to facilitate the recruitment of other protein factors. Here we describe the use of fluorescence resonance energy transfer (FRET) to evaluate DNA bending using TBP as a model system. FRET is a useful technique to measure changes in DNA conformation due to protein binding because small changes in the distance between two fluorophores (2-10 nm) translate into large changes in energy transfer.
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The regulation of mammalian mRNA transcription by lncRNAs: recent discoveries and current concepts.
Epigenomics
PUBLISHED: 02-19-2013
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Transcription by RNA Pol II is a tightly controlled process that is critical to normal cellular metabolism. Understanding how transcriptional regulation is orchestrated has mainly involved identifying and characterizing proteins that function as transcription factors. During the past decade, however, an increasing number of lncRNAs have been identified as transcriptional regulators. This revelation has spurred new discoveries, novel techniques and paradigm shifts, which together are redefining our understanding of transcriptional control and broadening our view of RNA function. Here, we summarize recent discoveries concerning the role of lncRNAs as regulators of mammalian mRNA transcription, with a focus on key concepts that are guiding current research in the field.
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The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II.
J. Mol. Biol.
PUBLISHED: 01-29-2013
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The B2 family of short interspersed elements is transcribed into non-coding RNA by RNA polymerase III. The ~180-nt B2 RNA has been shown to potently repress mRNA transcription by binding tightly to RNA polymerase II (Pol II) and assembling with it into complexes on promoter DNA, where it keeps the polymerase from properly engaging the promoter DNA. Mammalian Pol II is an ~500-kDa complex that contains 12 different protein subunits, providing many possible surfaces for interaction with B2 RNA. We found that the carboxy-terminal domain of the largest Pol II subunit was not required for B2 RNA to bind Pol II and repress transcription in vitro. To identify the surface on Pol II to which the minimal functional region of B2 RNA binds, we coupled multi-step affinity purification, reversible formaldehyde cross-linking, peptide sequencing by mass spectrometry, and analysis of peptide enrichment. The Pol II peptides most highly recovered after cross-linking to B2 RNA mapped to the DNA binding cleft and active-site region of Pol II. These studies determine the location of a defined nucleic acid binding site on a large, native, multi-subunit complex and provide insight into the mechanism of transcriptional repression by B2 RNA.
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A Case of Basilar Artery Aneurysm Rupture from 1836: Lessons in Clinical Observation and the Natural History of the Disease.
World Neurosurg
PUBLISHED: 01-19-2013
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Although credit is given to Sir William Gull for highlighting the clinical picture of subarachnoid hemorrhage in 1859, we discuss a case presented by Mr. Egerton A. Jennings, Fellow of the Linnaean Society, published 23 years earlier in the 1836 edition of the Transactions of the Provincial Medical and Surgical Association. This case, one of the first reported cases in the English language of a basilar aneurysm rupture, is of medico-historical interest. Jennings provided a remarkably accurate and detailed description of the patient, who experienced coma as a result of the severity of subarachnoid hemorrhage. The detailed clinical observations on initial assessment and the description of the patients deterioration to the time of death are a succinct representation of the natural history of this disease. The authors discussion provides evidence of a philosophy committed to medical education and progress at the time based on principles of rational observation, meticulous clinical acumen, insight into experimental physiology, and the awareness of ethical boundaries. In provincial 1836 England, similar to most of Europe, cerebral localization was elementary. Nonetheless, this case report highlights the attempt at linking structure to function by means of observation on the effects of lesioning. It provides evidence of an established thought process already in progress in England in the 19th century. It is characteristic that this thought process came from a surgical practitioner. The cultivation of practical observation in British surgical culture would allow the late 19th century surgeon scientists to match the contributions of British neurologists with landmark steps in the development and establishment of neurosurgery.
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RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA.
EMBO J.
PUBLISHED: 01-03-2013
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RNA polymerase II (Pol II) is a well-characterized DNA-dependent RNA polymerase, which has also been reported to have RNA-dependent RNA polymerase (RdRP) activity. Natural cellular RNA substrates of mammalian Pol II, however, have not been identified and the cellular function of the Pol II RdRP activity is unknown. We found that Pol II can use a non-coding RNA, B2 RNA, as both a substrate and a template for its RdRP activity. Pol II extends B2 RNA by 18 nt on its 3-end in an internally templated reaction. The RNA product resulting from extension of B2 RNA by the Pol II RdRP can be removed from Pol II by a factor present in nuclear extracts. Treatment of cells with ?-amanitin or actinomycin D revealed that extension of B2 RNA by Pol II destabilizes the RNA. Our studies provide compelling evidence that mammalian Pol II acts as an RdRP to control the stability of a cellular RNA by extending its 3-end.
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B2 RNA represses TFIIH phosphorylation of RNA polymerase II.
Transcription
PUBLISHED: 02-18-2011
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Mouse B2 RNA represses RNA polymerase II (Pol II) transcription during the cellular heat shock response. B2 RNA binds Pol II, enters complexes at promoters, and keeps the polymerase from engaging the DNA. Here we show that phosphorylation of Ser5 residues in the Pol II carboxy terminal domain (CTD) decreases after heat shock at the promoter of the repressed actin gene in mouse cells, despite the continued presence of Cdk7 and cyclin H. Biochemical assays revealed that B2 RNA, when present with Pol II in promoter-bound complexes, specifically represses CTD phosphorylation by TFIIH.
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DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration.
Nature
PUBLISHED: 01-18-2011
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Geographic atrophy (GA), an untreatable advanced form of age-related macular degeneration, results from retinal pigmented epithelium (RPE) cell degeneration. Here we show that the microRNA (miRNA)-processing enzyme DICER1 is reduced in the RPE of humans with GA, and that conditional ablation of Dicer1, but not seven other miRNA-processing enzymes, induces RPE degeneration in mice. DICER1 knockdown induces accumulation of Alu RNA in human RPE cells and Alu-like B1 and B2 RNAs in mouse RPE. Alu RNA is increased in the RPE of humans with GA, and this pathogenic RNA induces human RPE cytotoxicity and RPE degeneration in mice. Antisense oligonucleotides targeting Alu/B1/B2 RNAs prevent DICER1 depletion-induced RPE degeneration despite global miRNA downregulation. DICER1 degrades Alu RNA, and this digested Alu RNA cannot induce RPE degeneration in mice. These findings reveal a miRNA-independent cell survival function for DICER1 involving retrotransposon transcript degradation, show that Alu RNA can directly cause human pathology, and identify new targets for a major cause of blindness.
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XPB, a subunit of TFIIH, is a target of the natural product triptolide.
Nat. Chem. Biol.
PUBLISHED: 01-06-2011
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Triptolide (1) is a structurally unique diterpene triepoxide isolated from a traditional Chinese medicinal plant with anti-inflammatory, immunosuppressive, contraceptive and antitumor activities. Its molecular mechanism of action, however, has remained largely elusive to date. We report that triptolide covalently binds to human XPB (also known as ERCC3), a subunit of the transcription factor TFIIH, and inhibits its DNA-dependent ATPase activity, which leads to the inhibition of RNA polymerase II-mediated transcription and likely nucleotide excision repair. The identification of XPB as the target of triptolide accounts for the majority of the known biological activities of triptolide. These findings also suggest that triptolide can serve as a new molecular probe for studying transcription and, potentially, as a new type of anticancer agent through inhibition of the ATPase activity of XPB.
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Long-term visual safety of voriconazole in adult patients with paracoccidioidomycosis.
Clin Ther
PUBLISHED: 12-08-2010
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Voriconazole is an antifungal agent with in vitro activity and clinical efficacy against yeasts, molds, and dimorphic fungi (eg, Paracoccidioides brasiliensis). The safety profile of voriconazole includes transient visual adverse events (VAEs) that resolve while undergoing treatment or after its discontinuation.
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Hepatic safety and tolerability in the maraviroc clinical development program.
AIDS
PUBLISHED: 10-12-2010
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Maraviroc is the first CCR5 antagonist to be approved for the treatment of HIV-1 infection. It is generally well tolerated, with a similar side-effect profile to placebo in controlled studies. Many agents used to treat HIV disease are associated with the potential for hepatotoxicity. The hepatic effects of maraviroc were analyzed across all Pfizer-sponsored maraviroc clinical trials, in which 2350 volunteers received maraviroc. Although sporadic hepatic enzyme abnormalities were reported in 34 phase 1/2a studies of up to 28-day duration, they demonstrated no dose relationship or association with hyperbilirubinemia. In the four phase 2b/3 studies in antiretroviral -naive and antiretroviral-experienced patients, there was no significant imbalance in hepatic enzyme abnormalities or hepatobiliary adverse events in maraviroc versus comparator arms up to week 96. The findings were similar in patients coinfected with hepatitis B and/or C virus, although the number of coinfected patients was small. No patient met the strict definition for Hys Law. Two participants reported severe hepatotoxicity and although other potential causes were present, the contribution of maraviroc to these events could not be excluded. This analysis suggests that maraviroc does not present significant risks to hepatic safety when taken at the recommended doses in the populations studied.
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Impact of baseline antiretroviral resistance status on efficacy outcomes among patients receiving maraviroc plus optimized background therapy in the MOTIVATE 1 and 2 trials.
HIV Clin Trials
PUBLISHED: 08-26-2010
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The MOTIVATE studies assessed maraviroc with optimized background therapy (OBT) in treatment-experienced patients with R5 HIV-1. This post hoc analysis compared outcomes between patients with and without HIV-1 resistance to epsilon3 classes of antiretrovirals at screening (triple-class-resistant [TCR] versus not-TCR [nTCR]).
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Efficacy and safety of maraviroc versus efavirenz, both with zidovudine/lamivudine: 96-week results from the MERIT study.
HIV Clin Trials
PUBLISHED: 08-26-2010
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The MERIT study evaluated maraviroc versus efavirenz, both with zidovudine/lamivudine, in treatment-naïve patients with CCR5-tropic (R5) HIV-1. Post hoc analyses previously assessed week 48 outcomes in patients rescreened with R5 virus by a more sensitive tropism assay.
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Interparietal bone (Os Incae) in craniosynostosis.
Am. J. Med. Genet. A
PUBLISHED: 08-18-2010
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The interparietal bone, Os Incae, is formed in a persistent mendosal suture. This suture is a normal variant in the human skull, well-known in anatomy and radiology textbooks. We report 11 children with craniosynostosis in the presence of an interparietal bone, five from Childrens Hospital at Montefiore and six children from Childrens Hospital Boston. The true incidence of an interparietal bone in patients with craniosynostosis or craniofacial anomalies is not known; nor are there recognized sequelae of an interparietal bone (bathrocephaly). Hypotheses regarding mechanisms that may contribute to the formation of an interparietal bone are discussed.
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Two-year safety and virologic efficacy of maraviroc in treatment-experienced patients with CCR5-tropic HIV-1 infection: 96-week combined analysis of MOTIVATE 1 and 2.
J. Acquir. Immune Defic. Syndr.
PUBLISHED: 08-13-2010
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Maraviroc, the first approved CCR5 antagonist, demonstrated 48-week safety and virologic efficacy in CCR5-tropic HIV-infected, treatment-experienced patients; however, critical longer-term safety and durability of responses are unknown.
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Medical and surgical practice as represented in cultural figures from the pre-conquest Mesoamerican territories.
World Neurosurg
PUBLISHED: 07-20-2010
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To review medical and surgical practices in pre-Conquest Mexico in the Olmec and Mayan regions and areas of West Mexico as depicted on terra-cotta, stone, and stelae figures.
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Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation.
Nat. Rev. Genet.
PUBLISHED: 07-13-2010
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The eukaryotic core promoter recognition complex was generally thought to play an essential but passive role in the regulation of gene expression. However, recent evidence now indicates that core promoter recognition complexes together with non-prototypical subunits may have a vital regulatory function in driving cell-specific programmes of transcription during development. Furthermore, new roles for components of these complexes have been identified beyond development; for example, in mediating interactions with chromatin and in maintaining active gene expression across cell divisions.
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Genome-wide insights into eukaryotic transcriptional control.
Genome Biol.
PUBLISHED: 06-07-2010
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A report of the Keystone Symposium on Dynamics of Eukaryotic Transcription during Development, Big Sky, Montana, USA, 7-12 April 2010.
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Dampening DNA binding: a common mechanism of transcriptional repression for both ncRNAs and protein domains.
RNA Biol
PUBLISHED: 05-26-2010
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With eukaryotic non-coding RNAs (ncRNAs) now established as critical regulators of cellular transcription, the true diversity with which they can elicit biological effects is beginning to be appreciated. Two ncRNAs, mouse B2 RNA and human Alu RNA, have been found to repress mRNA transcription in response to heat shock. They do so by binding directly to RNA polymerase II, assembling into complexes on promoter DNA, and disrupting contacts between the polymerase and the DNA. Such a mechanism of repression had not previously been observed for a eukaryotic ncRNA; however, there are examples of eukaryotic protein domains that repress transcription by blocking essential protein-DNA interactions. Comparing the mechanism of transcriptional repression utilized by these protein domains to that used by B2 and Alu RNAs raises intriguing questions regarding transcriptional control, and how B2 and Alu RNAs might themselves be regulated.
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The C-terminal region of human NFATc2 binds cJun to synergistically activate interleukin-2 transcription.
Mol. Immunol.
PUBLISHED: 04-30-2010
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At eukaryotic promoters, multi-faceted protein-protein and protein-DNA interactions can result in synergistic transcriptional activation. NFAT and AP-1 proteins induce interleukin-2 (IL-2) transcription in stimulated T cells, but the contributions of individual members of these activator families to synergistically activating IL-2 transcription is not known. To investigate the combinatorial regulation of IL-2 transcription we tested the ability of different combinations of NFATc2, NFATc1, cJun, and cFos to synergistically activate transcription from the IL-2 promoter. We found that NFATc2 and cJun are exclusive in their ability to synergistically activate human IL-2 transcription. Protein-protein interaction assays revealed that in the absence of DNA, NFATc2, but not NFATc1, bound directly to cJun/cJun dimers, but not to cFos/cJun heterodimers. A region of NFATc2 C-terminal of the DNA binding domain was necessary and sufficient for interaction with cJun in the absence of DNA, and this same region of NFATc2 was required for the synergistic activation of IL-2 transcription in T cells. Moreover, expression of this C-terminal region of NFATc2 specifically repressed the synergistic activation of IL-2 transcription. These studies show that a previously unidentified interaction between human NFATc2 and cJun is necessary for synergistic activation of IL-2 transcription in T cells.
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Effects of maraviroc and efavirenz on markers of immune activation and inflammation and associations with CD4+ cell rises in HIV-infected patients.
PLoS ONE
PUBLISHED: 04-29-2010
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Maraviroc treatment for HIV-1 infected patients results in larger CD4(+) T cell rises than are attributable to its antiviral activity alone. We investigated whether this is due to modulation of T cell activation and inflammation.
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Maraviroc versus efavirenz, both in combination with zidovudine-lamivudine, for the treatment of antiretroviral-naive subjects with CCR5-tropic HIV-1 infection.
J. Infect. Dis.
PUBLISHED: 02-16-2010
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The MERIT (Maraviroc versus Efavirenz in Treatment-Naive Patients) study compared maraviroc and efavirenz, both with zidovudine-lamivudine, in antiretroviral-naive patients with R5 human immunodeficiency virus type 1 (HIV-1) infection.
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Development of the Metropolitan Water Availability Index (MWAI) and short-term assessment with multi-scale remote sensing technologies.
J. Environ. Manage.
PUBLISHED: 02-02-2010
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Global climate change will influence environmental conditions including temperature, surface radiation, soil moisture, and sea level, and it will also significantly impact regional-scale hydrologic processes such as evapotranspiration (ET), precipitation, runoff, and snowmelt. The quantity and quality of water available for drinking and other domestic usage is also likely to be affected by changes in these processes. Consequently, it is necessary to assess and reflect upon the challenges ahead for water infrastructure and the general public in metropolitan regions. One approach to the problem is to use index-based assessment, forecasting and planning. The drought indices previously developed were not developed for domestic water supplies, and thus are insufficient for the purpose of such an assessment. This paper aims to propose and develop a "Metropolitan Water Availability Index (MWAI)" to assess the status of both the quantity and quality of available potable water sources diverted from the hydrologic cycle in a metropolitan region. In this approach, the accessible water may be expressed as volume per month or week (i.e., m(3)/month or m(3)/week) relative to a prescribed historical record, and such a trend analysis may result in final MWAI values ranging from -1 to +1 for regional water management decision making. The MWAI computation uses data and information from both historical point measurements and spatial remote-sensing based monitoring. Variables such as precipitation, river discharge, and water quality changes at drinking water plant intakes at specific locations are past "point" measurements in MWAI calculations. On the other hand, remote sensing provides information on both spatial and temporal distributions of key variables. Examples of remote-sensing images and sensor network technologies are in-situ sensor networks, ground-based radar, air-borne aircraft, and even space-borne satellites. A case study in Tampa Bay, Florida is described to demonstrate the short-term assessment of the MWAI concept at a practical level. It is anticipated that such a forecasting methodology may be extended for middle-term and long-term water supply assessment.
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Genomic gems: SINE RNAs regulate mRNA production.
Curr. Opin. Genet. Dev.
PUBLISHED: 01-15-2010
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Mammalian short interspersed elements (SINEs) are abundant retrotransposons that have long been considered junk DNA; however, RNAs transcribed from mouse B2 and human Alu SINEs have recently been found to control mRNA production at multiple levels. Upon cell stress B2 and Alu RNAs bind RNA polymerase II (Pol II) and repress transcription of some protein-encoding genes. Bi-directional transcription of a B2 SINE establishes a boundary that places the growth hormone locus in a permissive chromatin state during mouse development. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity through exonization via alternative splicing. Given the diverse means by which SINE encoded RNAs impact production of mRNAs, this genomic junk is proving to contain hidden gems.
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RNA polymerase II and TAFs undergo a slow isomerization after the polymerase is recruited to promoter-bound TFIID.
J. Mol. Biol.
PUBLISHED: 01-12-2010
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Transcription of mRNA genes requires that RNA polymerase II (Pol II) and the general transcription factors assemble on promoter DNA to form an organized complex capable of initiating transcription. Biochemical studies have shown that Pol II and TFIID (transcription factor IID) contact overlapping regions of the promoter, leading to the question of how these large factors reconcile their promoter interactions during complex assembly. To investigate how the TAF (TATA-binding protein-associated factor) subunits of TFIID alter the kinetic mechanism by which complexes assemble on promoters, we used a highly purified human transcription system. We found that TAFs sharply decrease the rate at which Pol II, TFIIB, and TFIIF assemble on promoter-bound TFIID-TFIIA. Interestingly, the slow step in this process is not recruitment of these factors to the DNA, but rather a postrecruitment isomerization of protein-DNA contacts that occurs throughout the core promoter. Our findings support a model in which Pol II and the general transcription factors rapidly bind promoter-bound TFIID-TFIIA, after which complexes undergo a slow isomerization in which the TAFs reorganize their contacts with the promoter to allow Pol II to properly engage the DNA. In this manner, TAFs kinetically repress basal transcription.
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Anatomy, technology, art, and culture: toward a realistic perspective of the brain.
Neurosurg Focus
PUBLISHED: 09-03-2009
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In the 15th century, brain illustration began to change from a schematic system that involved scant objective rendering of the brain, to accurate depictions based on anatomical dissections that demanded significant artistic talent. Notable examples of this innovation are the drawings of Leonardo da Vinci (1498-1504), Andreas Vesalius association with the bottega of Titian to produce the drawings of Vesalius De humani corporis fabrica (1543), and Christopher Wrens illustrations for Thomas Willis Cerebri Anatome (1664). These works appeared during the Renaissance and Age of Enlightenment, when advances in brain imaging, or really brain rendering, reflected not only the abilities and dedications of the artists, but also the influences of important cultural and scientific factors. Anatomy and human dissection became popular social phenomena as well as scholarly pursuits, linked with the world of the fine arts. The working philosophy of these artists involved active participation in both anatomical study and illustration, and the belief that their discoveries of the natural world could best be communicated by rendering them in objective form (that is, with realistic perspective). From their studies emerged the beginning of contemporary brain imaging. In this article, the authors examine how the brain began to be imaged in realism within a cultural and scientific milieu that witnessed the emergence of anatomical dissection, the geometry of linear perspective, and the closer confluence of art and science.
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InvAluable junk: the cellular impact and function of Alu and B2 RNAs.
IUBMB Life
PUBLISHED: 07-22-2009
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The short interspersed elements (SINEs) Alu and B2 are retrotransposons that litter the human and mouse genomes, respectively. Given their abundance, the manner in which these elements impact the host genome and what their biological functions might be is of significant interest. Finding that Alu and B2 SINEs are transcribed, both as distinct RNA polymerase III transcripts and as part of RNA polymerase II transcripts, and that these SINE encoded RNAs indeed have biological functions has refuted the historical notion that SINEs are merely "junk DNA." This article reviews currently known cellular functions of both RNA polymerase II and RNA polymerase III transcribed Alu and B2 RNAs. These RNAs, in different forms, control gene expression by participating in processes as diverse as mRNA transcriptional control, A-to-I editing, nuclear retention, and alternative splicing. Future studies will likely reveal additional contributions of Alu and B2 RNAs as regulators of gene expression.
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From bacteria to humans, chromatin to elongation, and activation to repression: The expanding roles of noncoding RNAs in regulating transcription.
Crit. Rev. Biochem. Mol. Biol.
PUBLISHED: 05-20-2009
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Noncoding RNAs (ncRNAs) have emerged as key regulators of transcription, often functioning as trans-acting factors akin to prototypical protein transcriptional regulators. Inside cells, ncRNAs are now known to control transcription of single genes as well as entire transcriptional programs in response to developmental and environmental cues. In doing so, they target nearly all levels of the transcription process from regulating chromatin structure through controlling transcript elongation. Moreover, trans-acting ncRNA transcriptional regulators have been found in organisms as diverse as bacteria and humans. With the recent discovery that much of the DNA in genomes is transcribed into ncRNAs with yet unknown function, it is likely that future studies will reveal many more ncRNA regulators of transcription.
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A double-blind, placebo-controlled trial of maraviroc in treatment-experienced patients infected with non-R5 HIV-1.
J. Infect. Dis.
PUBLISHED: 05-13-2009
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Maraviroc, a CCR5 antagonist, is active against R5 but not X4 or dual- or mixed-tropic strains of human immunodeficiency virus type 1 (HIV-1). A phase 2b study was conducted to determine the safety and efficacy of maraviroc in combination with optimized background therapy in treatment-experienced patients infected with dual- or mixed-tropic HIV-1.
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Endovascular transvenous embolization of sinus pericranii. Case report.
J Neurosurg Pediatr
PUBLISHED: 04-03-2009
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Sinus pericranii (SP) is an abnormal communication between the intra- and extracranial venous drainage pathways. Treatment of this condition has mainly been recommended for reasons of cosmesis and prevention of hemorrhage. The authors report a novel endovascular transvenous route for definitive treatment of SP.
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B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 03-23-2009
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Noncoding RNAs (ncRNAs) are now recognized as transregulators of eukaryotic transcription, a role once attributed exclusively to protein factors. Two ncRNAs in mammalian cells have been shown to repress general mRNA transcription by RNA polymerase II (Pol II) in response to heat shock: mouse B2 RNA and human Alu RNA. B2 and Alu RNAs bind directly and tightly to Pol II and co-occupy the promoters of repressed genes along with the polymerase. Here, we identified the molecular mechanism by which mouse B2 RNA and human Alu RNA repress Pol II transcription. Biochemical assays to probe the network of protein-DNA interactions at the promoter revealed that B2 and Alu RNAs prevent Pol II from establishing contacts with the promoter both upstream and downstream of the TATA box during closed complex formation. Disruption of these contacts correlates with transcriptional repression. We conclude that B2 and Alu RNA prevent Pol II from properly engaging the DNA during closed complex formation, resulting in complexes with an altered conformation that are transcriptionally inert. In the absence of its normal contacts with the promoter, Pol II is likely held in these inactive complexes on DNA through interactions with promoter-bound TATA box-binding protein and transcription factor IIB.
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TATA-binding protein and transcription factor IIB induce transcript slipping during early transcription by RNA polymerase II.
J. Biol. Chem.
PUBLISHED: 02-04-2009
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To better understand the mechanism of steps in early transcription by RNA polymerase II (pol II), we investigated the molecular determinants of transcript slipping within complexes assembled on promoters containing a pre-melted transcription bubble from -9 to +3. Transcript slippage occurs when an RNA transcript contains a repetitive sequence that allows the transcript to slip back and pair with the template strand of the DNA at a new register before transcription continues. We established the contributions of individual transcription factors, DNA elements, and RNA length to slipping on a heteroduplex template using a highly purified human pol II transcription system. We found that transcripts slip at a very defined point in the transcription reaction, after pol II completes phosphodiester bond synthesis at register +5. This point is set by the position of the polymerase active site on the DNA template, as opposed to the length of the transcript, as well as by a repetitive CUCU sequence that must occur from +2 to +5. Interestingly, slipping at this juncture is induced by TATA-binding protein and transcription factor IIB and requires a TATA box but not a transcription factor IIB recognition sequence. We propose a model in which transcribing complexes, upon completing phosphodiester bond synthesis at register +5, enter one of two branches in which they either complete productive synthesis of the transcript or undergo multiple rounds of transcript slipping.
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Real-time contaminant detection and classification in a drinking water pipe using conventional water quality sensors: techniques and experimental results.
J. Environ. Manage.
PUBLISHED: 01-21-2009
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Accurate detection and identification of natural or intentional contamination events in a drinking water pipe is critical to drinking water supply security and health risk management. To use conventional water quality sensors for the purpose, we have explored a real-time event adaptive detection, identification and warning (READiw) methodology and examined it using pilot-scale pipe flow experiments of 11 chemical and biological contaminants each at three concentration levels. The tested contaminants include pesticide and herbicides (aldicarb, glyphosate and dicamba), alkaloids (nicotine and colchicine), E. coli in terrific broth, biological growth media (nutrient broth, terrific broth, tryptic soy broth), and inorganic chemical compounds (mercuric chloride and potassium ferricyanide). First, through adaptive transformation of the sensor outputs, contaminant signals were enhanced and background noise was reduced in time-series plots leading to detection and identification of all simulated contamination events. The improved sensor detection threshold was 0.1% of the background for pH and oxidation-reduction potential (ORP), 0.9% for free chlorine, 1.6% for total chlorine, and 0.9% for chloride. Second, the relative changes calculated from adaptively transformed residual chlorine measurements were quantitatively related to contaminant-chlorine reactivity in drinking water. We have shown that based on these kinetic and chemical differences, the tested contaminants were distinguishable in forensic discrimination diagrams made of adaptively transformed sensor measurements.
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Separation of craniopagus conjoined twins with a staged approach.
J Craniofac Surg
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The separation of craniopagus conjoined twins is a very rare and complex challenge. As with many rare challenges, it presents initially as a deceptively simple problem requiring only the most basic clinical techniques. As in many reconstructive problems, this paradigm mandates that the neurosurgical team performs the separation with the plastic surgeons providing closure at the end of the separation. Historically, these approaches have included, as with the separation of many other types of conjoined twins, the use of tissue expansion before separation followed by separation surgery. In the best hands, at the most capable medical centers, the mortality reported in the literature for the past 50 years is greater than 50%. Craniofacial surgery frequently demands a coordinated effort between plastic surgery and neurosurgery and many other specializations; separating craniopagus twins takes this coordination to a stratospheric level. It is, however, this coordination that is of paramount importance. Success clearly requires an understanding of the complex interrelationship between the "separation" and the "reconstruction" and that decisions made for 1 aspect of the surgery will have a profound impact on another aspect of the surgery. The impact can be disastrous or, if planned well, can be advantageous.We were contacted to evaluate craniopagus conjoined male infant twins for separation. Radiographic studies suggested that the brains were separate, and their medical team suggested that they were "fit for separation." We reviewed the literature and reviewed our colleagues experiences with similar cases around the world. It became clear that whether separation had been unsuccessful or successful, a variety of issues accompanied surgery as follows: (1) massive intraoperative hemorrhage, (2) cerebral edema, (3) venous infarcts, (4) swelling of flaps, and (5) dehiscence of repairs with cerebrospinal fluid (CSF) leak, meningitis, or brain exposure. Although the initial plan was to separate the twins in the same fashion as in previous cases (ie, single-stage separation surgery preceded by tissue expansion of the scalp), it was clear that this approach increases cerebral venous pressure during the separation component of surgery and therefore set up a cascade of events favoring failure rather than success. Wishing to favor success, we elected to design an open-ended multistaged separation to improve venous collateral circulation. We believe that this would improve venous drainage, prevent increased venous pressure, diminish cerebral edema, and favor the integrity of the dura and flap repair that would in turn lessen the risk of CSF leak. The stages would also allow the twins to recover from each stage before progressing to the next stage while continuing to receive nutritional support and physical therapy. Four major stages for 9 ½ months led to their successful separation. There has been no CSF leak or meningitis. To our knowledge, this technique has since been applied to 2 other sets of craniopagus with similar outcomes.A review of the pertinent literature, our rationale, and methodology are discussed in this article.
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Structural insights into transcriptional repression by noncoding RNAs that bind to human Pol II.
J. Mol. Biol.
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Gene transcription is regulated in response to environmental changes and developmental cues. In mammalian cells subjected to stress conditions such as heat shock, transcription of most protein-coding genes decreases, while the transcription of heat shock protein genes increases. Repression involves direct binding to RNA polymerase II (Pol II) of certain noncoding RNAs (ncRNAs) that are upregulated upon heat shock. Another class of ncRNAs is also upregulated and binds to Pol II but does not inhibit transcription. Incorporation of repressive ncRNAs into pre-initiation complexes prevents transcription initiation, while non-repressive ncRNAs are displaced from Pol II by TFIIF. Here, we present cryo-electron microscopy reconstructions of human Pol II in complex with six different ncRNAs from mouse and human. Our structures show that both repressive and non-repressive ncRNAs bind to a conserved binding site within the cleft of Pol II. The site, which is also shared with a previously characterized yeast aptamer, is close to the active center and, thus, in an ideal position to regulate transcription. Importantly, additional RNA elements extend flexibly beyond the docking site. We propose that the differences concerning the repressive activity of the ncRNAs analyzed must be due to the distinct character of these more unstructured, flexible segments of the RNA that emanate from the cleft.
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Single-molecule fluorescence resonance energy transfer shows uniformity in TATA binding protein-induced DNA bending and heterogeneity in bending kinetics.
Biochemistry
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TATA binding protein (TBP) is a key component of the eukaryotic RNA polymerase II transcription machinery that binds to TATA boxes located in the core promoter regions of many genes. Structural and biochemical studies have shown that when TBP binds DNA, it sharply bends the DNA. We used single-molecule fluorescence resonance energy transfer (smFRET) to study DNA bending by human TBP on consensus and mutant TATA boxes in the absence and presence of TFIIA. We found that the state of the bent DNA within populations of TBP-DNA complexes is homogeneous; partially bent intermediates were not observed. In contrast to the results of previous ensemble studies, TBP was found to bend a mutant TATA box to the same extent as the consensus TATA box. Moreover, in the presence of TFIIA, the extent of DNA bending was not significantly changed, although TFIIA did increase the fraction of DNA molecules bound by TBP. Analysis of the kinetics of DNA bending and unbending revealed that on the consensus TATA box two kinetically distinct populations of TBP-DNA complexes exist; however, the bent state of the DNA is the same in the two populations. Our smFRET studies reveal that human TBP bends DNA in a largely uniform manner under a variety of different conditions, which was unexpected given previous ensemble biochemical studies. Our new observations led to us to revise the model for the mechanism of DNA binding by TBP and for how DNA bending is affected by TATA sequence and TFIIA.
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ERK1/2 activation is a therapeutic target in age-related macular degeneration.
Proc. Natl. Acad. Sci. U.S.A.
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Deficient expression of the RNase III DICER1, which leads to the accumulation of cytotoxic Alu RNA, has been implicated in degeneration of the retinal pigmented epithelium (RPE) in geographic atrophy (GA), a late stage of age-related macular degeneration that causes blindness in millions of people worldwide. Here we show increased extracellular-signal-regulated kinase (ERK) 1/2 phosphorylation in the RPE of human eyes with GA and that RPE degeneration in mouse eyes and in human cell culture induced by DICER1 depletion or Alu RNA exposure is mediated via ERK1/2 signaling. Alu RNA overexpression or DICER1 knockdown increases ERK1/2 phosphorylation in the RPE in mice and in human cell culture. Alu RNA-induced RPE degeneration in mice is rescued by intravitreous administration of PD98059, an inhibitor of the ERK1/2-activating kinase MEK1, but not by inhibitors of other MAP kinases such as p38 or JNK. These findings reveal a previously unrecognized function of ERK1/2 in the pathogenesis of GA and provide a mechanistic basis for evaluation of ERK1/2 inhibition in treatment of this disease.
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Germline mosacism in Shprintzen-Goldberg syndrome.
Am. J. Med. Genet. A
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We report on maternal half-sibs born to unaffected, non-consanguineous parents with classical Shprintzen-Goldberg syndrome (SGS) who had in addition intestinal malrotation and an aberrant subclavian artery. In one other SGS family germline mosaicism has been described. SGS is molecularly heterogeneous and has been linked to mutations in three genomic loci. This suggests there may be multiple other genetic factors that result in a common clinical phenotype and a number of investigators have implicated a fourth region (15q25-qter) in the etiology of SGS.
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Marvelous medicine: the untold story of the Wade-Dahl-Till valve.
J Neurosurg Pediatr
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On December 5, 1960, 4-month-old Theo Dahl, the only son of best-selling author Roald Dahl (1916-1990), had his skull shattered in a horrific traffic accident. What began as a personal tragedy for the Dahl family would soon evolve into a dogged crusade by Dahl to expand upon preexisting valve technology with the goal of developing a shunt that would not become obstructed. Based upon exclusive access to private archives of the Dahl estate, as well as interviews with those involved, this article tells the intricate tale of one famous fathers drive to significantly alter the natural history of pediatric hydrocephalus. Dahls collaboration with British toymaker Stanley Wade and pioneering pediatric neurosurgeons Joseph Ransohoff, Kenneth Shulman, and Kenneth Till to create the Wade-Dahl-Till (WDT) valve is examined in detail. The ensuing rift between the American and British contingents, the valves multiple design revisions, and the goal of creating an affordable shunt for children in developing countries are among the issues addressed. The development of the WDT valve marked a significant turning point in the surgical management of pediatric hydrocephalus in general and in shunt valve technology in particular.
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DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88.
Cell
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Alu RNA accumulation due to DICER1 deficiency in the retinal pigmented epithelium (RPE) is implicated in geographic atrophy (GA), an advanced form of age-related macular degeneration that causes blindness in millions of individuals. The mechanism of Alu RNA-induced cytotoxicity is unknown. Here we show that DICER1 deficit or Alu RNA exposure activates the NLRP3 inflammasome and triggers TLR-independent MyD88 signaling via IL18 in the RPE. Genetic or pharmacological inhibition of inflammasome components (NLRP3, Pycard, Caspase-1), MyD88, or IL18 prevents RPE degeneration induced by DICER1 loss or Alu RNA exposure. These findings, coupled with our observation that human GA RPE contains elevated amounts of NLRP3, PYCARD, and IL18 and evidence of increased Caspase-1 and MyD88 activation, provide a rationale for targeting this pathway in GA. Our findings also reveal a function of the inflammasome outside the immune system and an immunomodulatory action of mobile elements.
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Non-coding RNAs: key regulators of mammalian transcription.
Trends Biochem. Sci.
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Non-coding RNAs (ncRNAs) are now recognized as active participants in controlling many biological processes. Indeed, these products of transcription can even control the process of transcription itself. In the past several years, ncRNAs have been found to regulate transcription of single genes, as well as entire transcriptional programs, affecting the expression of hundreds to thousands of genes in response to developmental or environmental signals. Compared to more classical protein regulators, the list of ncRNAs that regulate mRNA transcription in mammalian cells is still small; however, the rate at which new ncRNA transcriptional regulators are being discovered is rapid, suggesting that models for how gene expression is controlled will continue to be redefined as this field develops.
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Maraviroc, a chemokine receptor-5 antagonist, fails to demonstrate efficacy in the treatment of patients with rheumatoid arthritis in a randomized, double-blind placebo-controlled trial.
Arthritis Res. Ther.
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The purpose of this study was to determine whether maraviroc, a human CC chemokine receptor 5 (CCR5) antagonist, is safe and effective in the treatment of active rheumatoid arthritis (RA) in patients on background methotrexate (MTX).
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.