Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development

During differentiation of embryonic stem cells, chromatin reorganizes to establish cell type-specific expression programs. Here, we have dissected the linkages between DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome repositioning, and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we found that the interplay between these factors depends on their genomic context. The mostly unmethylated CpG islands have reduced nucleosome occupancy and are enriched in cell type-independent binding sites for CTCF. The few remaining methylated CpG dinucleotides are preferentially associated with nucleosomes. In contrast, outside of CpG islands most CpGs are methylated, and the average methylation density oscillates so that it is highest in the linker region between nucleosomes. Outside CpG islands, binding of TET1, an enzyme that converts 5mC to 5hmC, is associated with labile, MNase-sensitive nucleosomes. Such nucleosomes are poised for eviction in ESCs and become stably bound in differentiated cells where the TET1 and 5hmC levels go down. This process regulates a class of CTCF binding sites outside CpG islands that are occupied by CTCF in ESCs but lose the protein during differentiation. We rationalize this cell type-dependent targeting of CTCF with a quantitative biophysical model of competitive binding with the histone octamer, depending on the TET1, 5hmC, and 5mC state

Coding RNAs with a non-coding function: Maintenance of open chromatin structure

The multi-layered organization of the genome in a large nucleoprotein complex termed chromatin regulates nuclear functions by establishing subcompartments with distinct DNA-associated activities. Here, we demonstrate that RNA plays an important role in maintaining a decondensed and biologically active interphase chromatin conformation in human and mouse cell lines. As shown by RNase A microinjection and fluorescence microscopy imaging, digestion of single-stranded RNAs induced a distinct micrometer scale chromatin aggregation of these decondensed regions. In contrast, pericentric heterochromatin was more resistant to RNase A treatment. We identified a class of coding RNA transcripts that are responsible for this activity, and thus termed these ‘chromatin-interlinking’ RNAs or ciRNAs. The initial chromatin distribution could be restored after RNase A treatment with a purified nuclear RNA fraction that was analyzed by high-throughput sequencing. It comprised long >500 nucleotides (nt) RNA polymerase II (RNAP II) transcripts that were spliced, depleted of polyadenylation and was enriched with long 3'-untranslated regions (3’-UTRs) above ~800 nt in length. Furthermore, similar reversible changes of the chromatin conformation and the RNAP II distribution were induced by either RNA depletion or RNAP II inhibition. Based on these results we propose that ciRNAs could act as genome organizing architectural factors of actively transcribed chromatin compartments

Nurses Alumni Association Bulletin, Fall 1982

Alumni Calendar Officers and Chairmen of Committees Letter from the President School of Nursing Annual Report to the Alumni Association 1980-1981 Thomas Jefferson University, College of Allied Health Sciences- School of Nursing Awards 1982 Historical Highlights, Jefferson School of Nursing The History of the Jefferson Cap Two Firsts for Doris Bowman Congratulations, Jeraldine Kohut Tribute to Elizabeth Sweeney 1982 Commencement Address Nero Fiddles While Rome Burns A Fiftieth Reunion Fiftieth Anniversary- Class of 1932 White Haven Alumnae Celebrate 35th Anniversary Treasurers\u27 Financial Report Social Report Scholarship Report Report of Sick and Welfare Committee Martha Riland Reports Nurses\u27 Relief Fund Nurses\u27 Scholarship Fund Resume\u27 of Minutes of Alumni Association Meetings Happy Birthday Finance Committee Report Pictures, Luncheon School of Nursing, Graduates 1982 Class Notes In Memoriam, Names of Deceased Members Notices Change of Address For

Mycobacterium leprae Phenolglycolipid-1 Expressed by Engineered M. bovis BCG Modulates Early Interaction with Human Phagocytes

The species-specific phenolic glycolipid 1 (PGL-1) is suspected to play a critical role in the pathogenesis of leprosy, a chronic disease of the skin and peripheral nerves caused by Mycobacterium leprae. Based on studies using the purified compound, PGL-1 was proposed to mediate the tropism of M. leprae for the nervous system and to modulate host immune responses. However, deciphering the biological function of this glycolipid has been hampered by the inability to grow M. leprae in vitro and to genetically engineer this bacterium. Here, we identified the M. leprae genes required for the biosynthesis of the species-specific saccharidic domain of PGL-1 and reprogrammed seven enzymatic steps in M. bovis BCG to make it synthesize and display PGL-1 in the context of an M. leprae-like cell envelope. This recombinant strain provides us with a unique tool to address the key questions of the contribution of PGL-1 in the infection process and to study the underlying molecular mechanisms. We found that PGL-1 production endowed recombinant BCG with an increased capacity to exploit complement receptor 3 (CR3) for efficient invasion of human macrophages and evasion of inflammatory responses. PGL-1 production also promoted bacterial uptake by human dendritic cells and dampened their infection-induced maturation. Our results therefore suggest that M. leprae produces PGL-1 for immune-silent invasion of host phagocytic cells

Genomics Meets Glycomics—The First GWAS Study of Human N-Glycome Identifies HNF1α as a Master Regulator of Plasma Protein Fucosylation

Over half of all proteins are glycosylated, and alterations in glycosylation have been observed in numerous physiological and pathological processes. Attached glycans significantly affect protein function; but, contrary to polypeptides, they are not directly encoded by genes, and the complex processes that regulate their assembly are poorly understood. A novel approach combining genome-wide association and high-throughput glycomics analysis of 2,705 individuals in three population cohorts showed that common variants in the Hepatocyte Nuclear Factor 1α (HNF1α) and fucosyltransferase genes FUT6 and FUT8 influence N-glycan levels in human plasma. We show that HNF1α and its downstream target HNF4α regulate the expression of key fucosyltransferase and fucose biosynthesis genes. Moreover, we show that HNF1α is both necessary and sufficient to drive the expression of these genes in hepatic cells. These results reveal a new role for HNF1α as a master transcriptional regulator of multiple stages in the fucosylation process. This mechanism has implications for the regulation of immunity, embryonic development, and protein folding, as well as for our understanding of the molecular mechanisms underlying cancer, coronary heart disease, and metabolic and inflammatory disorders

Ergebnisbericht der Online-Studie "Cyberbullying bei Schülerinnen und Schülern"

Sitzer P, Marth J, Kocik C, Müller KN. Ergebnisbericht der Online-Studie "Cyberbullying bei Schülerinnen und Schülern". IKG Forschungsbericht.; 2012

Formas utilizadas para tentativa de suicídio e características sociodemográficas de pacientes atendidos no serviço de emergência de um hospital de ensino

Aims: To assess the methods used in suicide attempts and sociodemographic characteristics of suicidal patients treated at the emergency department of a teaching hospital.Methods: Cross-sectional retrospective study, with active search for electronic medical records of patients treated at the emergency department of a public teaching hospital in the countryside of Rio Grande do Sul, Brazil, from January to December 2015. All cases of suicide attempt were included, regardless of the suicide methods used. Successful suicide cases were not investigated. The statistical analyses included descriptive statistics, univariate analysis, and Pearson’s chi-square test.Results: A total of 233 patients treated at the emergency department were referred for psychiatric evaluation, and 122 of them had attempted suicide. The mean age of the suicidal patients was 36.8±14.3 years, (minimum of 14 years and maximum of 88 years) and 74 (60.6%) of them were female. The most common suicide attempt methods were ingestion of medications (72 cases, 59%) and of pesticide (14 cases, 11.5%). Of all patients, 119 (97.5%) lived in Santa Cruz do Sul, predominantly in the urban area (103 patients, 84.4%). Of the 50 (41.0%) referrals, 32 (64.0%) were sent to the Center for Psychosocial Care, 7 (14%) to the Center for Children’s and Adolescents’ Psychosocial Care, 6 (12%) were admitted to a mental health unit, and 5 (10%) were sent to Psychosocial Care Center for Alcohol and Drug Abuse. Sixty-six (54.1%) patients had no electronic medical records of their outcome after discharge and 6 (4.9%) were lost to follow-up.Conclusions: Most of the treated suicidal patients were young adult females. The most common method of suicide attempt was the ingestion of medications, followed by the ingestion of pesticides.Objetivos: Caracterizar as formas utilizadas para tentativa de suicídio e características sociodemográficas de pacientes atendidos no serviço de emergência de um hospital de ensino.Métodos: Estudo transversal retrospectivo, com busca ativa em prontuários eletrônicos de pacientes atendidos entre janeiro e dezembro de 2015 no serviço de emergência de um hospital de ensino que integra a rede pública de saúde do interior do estado do Rio Grande do Sul, Brasil. Foram incluídos todos os casos de tentativa de suicídio, independente de sua forma. Não foram investigados os casos que resultaram em óbito por suicídio. Foi utilizada estatística descritiva e foram avaliadas associações por análise univariada, sendo aplicado o teste do qui-quadrado de Pearson.Resultados: No período estudado foram encaminhados 233 pacientes atendidos na emergência para realização de avaliação psiquiátrica, sendo 122 casos caracterizados por tentativa de suicídio. Desses, a média de idade dos pacientes foi de 36,8±14,3 anos, com mínima de 14 e máxima de 88 anos e, 74 (60,6%) eram do sexo feminino. As formas mais utilizadas de tentativa de suicídio foram ingesta de medicamentos (72 casos, 59%) e ingesta de agrotóxicos (14 casos, 11,5%). Do total de pacientes, 119 (97,5%) residiam no município de Santa Cruz do Sul, com predominância nos moradores da zona urbana (103 pacientes, 84,4%). Dos 50 (41,0%) encaminhamentos, 32 (64,0%) foram para o Centro de Atendimento Psicossocial, 7 (14%) para Centro de Atendimento Psicossocial da Infância e Adolescência, 6 (12%) para internação em unidade de saúde mental e 5 (10%) para o Centro de Atendimento Psicossocial Álcool e Drogas. Em 66 (54,1%) pacientes não foi encontrado nenhum registro em prontuário eletrônico sobre o desfecho após a alta e 6 (4,9%) pacientes evadiram.Conclusões: A maioria dos pacientes atendidos por tentativa de suicídio foram adultos jovens do sexo feminino. Como principal forma utilizada para a tentativa de suicídio identificou-se a ingesta de medicamentos e em seguida a de agrotóxicos