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91.
Vicky Cho Yan Mei Arleen Sanny Stephanie Chan Anselm Enders Edward M Bertram Andy Tan Christopher C Goodnow T Daniel Andrews 《Genome biology》2014,15(1):R26
Background
Retention of a subset of introns in spliced polyadenylated mRNA is emerging as a frequent, unexplained finding from RNA deep sequencing in mammalian cells.Results
Here we analyze intron retention in T lymphocytes by deep sequencing polyadenylated RNA. We show a developmentally regulated RNA-binding protein, hnRNPLL, induces retention of specific introns by sequencing RNA from T cells with an inactivating Hnrpll mutation and from B lymphocytes that physiologically downregulate Hnrpll during their differentiation. In Ptprc mRNA encoding the tyrosine phosphatase CD45, hnRNPLL induces selective retention of introns flanking exons 4 to 6; these correspond to the cassette exons containing hnRNPLL binding sites that are skipped in cells with normal, but not mutant or low, hnRNPLL. We identify similar patterns of hnRNPLL-induced differential intron retention flanking alternative exons in 14 other genes, representing novel elements of the hnRNPLL-induced splicing program in T cells. Retroviral expression of a normally spliced cDNA for one of these targets, Senp2, partially corrects the survival defect of Hnrpll-mutant T cells. We find that integrating a number of computational methods to detect genes with differentially retained introns provides a strategy to enrich for alternatively spliced exons in mammalian RNA-seq data, when complemented by RNA-seq analysis of purified cells with experimentally perturbed RNA-binding proteins.Conclusions
Our findings demonstrate that intron retention in mRNA is induced by specific RNA-binding proteins and suggest a biological significance for this process in marking exons that are poised for alternative splicing. 相似文献92.
Vicky Dritsou Elena Deligianni Emmanuel Dialynas James Allen Nikos Poulakakis Christos Louis Dan Lawson Pantelis Topalis 《BMC genomics》2014,15(1)
Background
Only a small fraction of the mosquito species of the genus Anopheles are able to transmit malaria, one of the biggest killer diseases of poverty, which is mostly prevalent in the tropics. This diversity has genetic, yet unknown, causes. In a further attempt to contribute to the elucidation of these variances, the international “Anopheles Genomes Cluster Consortium” project (a.k.a. “16 Anopheles genomes project”) was established, aiming at a comprehensive genomic analysis of several anopheline species, most of which are malaria vectors. In the frame of the international consortium carrying out this project our team studied the genes encoding families of non-coding RNAs (ncRNAs), concentrating on four classes: microRNA (miRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), and in particular small nucleolar RNA (snoRNA) and, finally, transfer RNA (tRNA).Results
Our analysis was carried out using, exclusively, computational approaches, and evaluating both the primary NGS reads as well as the respective genome assemblies produced by the consortium and stored in VectorBase; moreover, the results of RNAseq surveys in cases in which these were available and meaningful were also accessed in order to obtain supplementary data, as were “pre-genomic era” sequence data stored in nucleic acid databases. The investigation included the identification and analysis, in most species studied, of ncRNA genes belonging to several families, as well as the analysis of the evolutionary relations of some of those genes in cross-comparisons to other members of the genus Anopheles.Conclusions
Our study led to the identification of members of these gene families in the majority of twenty different anopheline taxa. A set of tools for the study of the evolution and molecular biology of important disease vectors has, thus, been obtained.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1038) contains supplementary material, which is available to authorized users. 相似文献93.
Janneke H. H. M. van de Wijgert Hanneke Borgdorff Rita Verhelst Tania Crucitti Suzanna Francis Hans Verstraelen Vicky Jespers 《PloS one》2014,9(8)
We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB. 相似文献
94.
Vicky P. Chen Heidi Q. Xie Wallace K. B. Chan K. Wing Leung Gallant K. L. Chan Roy C. Y. Choi Suzanne Bon Jean Massoulié Karl W. K. Tsim 《The Journal of biological chemistry》2010,285(35):27265-27278
Acetylcholinesterase (AChE) is anchored onto cell membranes by the transmembrane protein PRiMA (proline-rich membrane anchor) as a tetrameric globular form that is prominently expressed in vertebrate brain. In parallel, the PRiMA-linked tetrameric butyrylcholinesterase (BChE) is also found in the brain. A single type of AChE-BChE hybrid tetramer was formed in cell cultures by co-transfection of cDNAs encoding AChET and BChET with proline-rich attachment domain-containing proteins, PRiMA I, PRiMA II, or a fragment of ColQ having a C-terminal GPI addition signal (QN-GPI). Using AChE and BChE mutants, we showed that AChE-BChE hybrids linked with PRiMA or QN-GPI always consist of AChET and BChET homodimers. The dimer formation of AChET and BChET depends on the catalytic domains, and the assembly of tetramers with a proline-rich attachment domain-containing protein requires the presence of C-terminal “t-peptides” in cholinesterase subunits. Our results indicate that PRiMA- or ColQ-linked cholinesterase tetramers are assembled from AChET or BChET homodimers. Moreover, the PRiMA-linked AChE-BChE hybrids occur naturally in chicken brain, and their expression increases during development, suggesting that they might play a role in cholinergic neurotransmission. 相似文献
95.
Summary A gene from Pseudomonas putida coding for a dehalogenase capable of degrading 2,2 dichloropropionic acid (2,2DCPA), the active ingredient of the herbicide dalapon, has been isolated and characterised. In plant transformation experiments the gene was shown to confer resistance to 2,2DCPA at a tissue culture level where 2,2DCPA could be used to select for transformants. At the whole plant level, transformed plants showed resistance to 2,2DCPA at concentrations up to 5 times the recommended dose rate of dalapon when it was sprayed on their leaves. At lower concentrations, the herbicide caused a non-lethal yellowing of sensitive plants which clearly distinguished them from resistant plants. The mode of action of chlorinated aliphatic acids is not known but they probably affect many enzyme pathways. The results described here are the first example of engineering a plant resistant to a herbicide that does not have one specific enzyme as its target site. This gene has several advantages as a marker in plant breeding and genetic studies. For example, the herbicide is readily available and has low toxicity, transformants can be selected at both the tissue culture and the whole plant level, a large number of transformed plants can easily be screened even in the field, and there is a very low probability of selecting spontaneous mutants.Abbreviations 2MCPA
2, monochloropropionic acid
- 2,2DCPA
2,2 dichloropropionic acid
- TCA
trichloroacetic acid 相似文献
96.
97.
K. G. Nicholson J. Kent V. Hammersley E. Cancio 《BMJ (Clinical research ed.)》1996,313(7065):1119-1123
OBJECTIVE: To assess the role of rhinoviruses in elderly people living in the community. DESIGN: Prospective community based surveillance of elderly people, without intervention. Subjects were telephoned weekly to identify symptomatic upper respiratory tract infections. Symptoms and impact of illnesses were monitored, and specimens were collected for diagnostic serology and human rhinovirus polymerase chain reaction. SETTING: Leicestershire, England. SUBJECTS: 533 subjects aged 60 to 90. MAIN OUTCOME MEASURES: Symptoms, restriction of activity, medical consultations, and antibiotic use during 96 rhinovirus infections. Adjusted odds ratios for lower respiratory syndromes with respect to smoking and health status. RESULTS: A viral cause was established in 211 (43%) of 497 respiratory illnesses; rhinoviruses were identified in 121 (24%) and as single pathogens in 107. The median duration of the first or only rhinovirus infection in the 96 people with 107 rhinovirus infections was 16 days; 18 of the 96 patients were confined to bed and 25 were unable to cope with routine household activities. Overall, 60 patients with rhinovirus infections had lower respiratory tract syndromes; 41 patients consulted their doctor, 31 of them (76%) receiving antibiotics. One patient died. Logistic regression analysis showed that chronic medical conditions increased the estimated probability of lower respiratory rhinovirus illness by 40% (95% confidence interval 17% to 68%) and smoking by 47% (14% to 90%). There were almost six times as many symptomatic rhinovirus infections as influenza A and B infections. CONCLUSIONS: Rhinoviruses are an important cause of debility and lower respiratory illness among elderly people in the community. Chronic ill health and smoking increase the likelihood of lower respiratory complications from such infections. The overall burden of rhinovirus infections in elderly people may approach that of influenza. 相似文献
98.
Christiane Roscher Vicky M. Temperton Michael Scherer-Lorenzen Martin Schmitz Jens Schumacher Bernhard Schmid Nina Buchmann Wolfgang W. Weisser Ernst-Detlef Schulze 《Ecology letters》2005,8(4):419-429
In a large integrated biodiversity project (‘The Jena Experiment’ in Germany) we established two experiments, one with a pool of 60 plant species that ranged broadly from dominant to subordinate competitors on large 20 × 20 m and small 3.5 × 3.5 m plots (= main experiment), and one with a pool of nine potentially dominant species on small 3.5 × 3.5 m plots (= dominance experiment). We found identical positive species richness–aboveground productivity relationships in the main experiment at both scales. This result suggests that scaling up, at least over the short term, is appropriate in interpreting the implications of such experiments for larger‐scale patterns. The species richness–productivity relationship was more pronounced in the experiment with dominant species (46.7 and 82.6% yield increase compared to mean monoculture, respectively). Additionally, transgressive overyielding occurred more frequently in the dominance experiment (67.7% of cases) than in the main experiment (23.4% of cases). Additive partitioning and relative yield total analyses showed that both complementarity and selection effects contributed to the positive net biodiversity effect. 相似文献
99.
Adam Walker Chun-Wa Chung Margarete Neu Manish Burman Thil Batuwangala Gavin Jones Chi-Man Tang Michael Steward Michael Mullin Nadia Tournier Alan Lewis Justyna Korczynska Vicky Chung Ian Catchpole 《The Journal of biological chemistry》2016,291(11):5500-5511
A potent VEGF inhibitor with novel antibody architecture and antigen binding mode has been developed. The molecule, hereafter referred to as VEGF dual dAb (domain antibody), was evaluated in vitro for binding to VEGF and for potency in VEGF-driven models and compared with other anti-VEGF biologics that have been used in ocular anti-angiogenic therapeutic regimes. VEGF dual dAb is more potent than bevacizumab and ranibizumab for VEGF binding, inhibition of VEGF receptor binding assays (RBAs), and VEGF-driven in vitro models of angiogenesis and displays comparable inhibition to aflibercept (Eylea). VEGF dual dAb is dimeric, and each monomer contains two distinct anti-VEGF domain antibodies attached via linkers to a human IgG1 Fc domain. Mechanistically, the enhanced in vitro potency of VEGF dual dAb, in comparison to other anti-VEGF biologics, can be explained by increased binding stoichiometry. A consistent model of the target engagement has been built based on the x-ray complexes of each of the two isolated domain antibodies with the VEGF antigen. 相似文献
100.
Daniel Stoessel Cameron J. Nowell Amy J. Jones Lori Ferrins Katherine M. Ellis Jennifer Riley Raphael Rahmani Kevin D. Read Malcolm J. McConville Vicky M. Avery Jonathan B. Baell Darren J. Creek 《Metabolomics : Official journal of the Metabolomic Society》2016,12(7):126