A Barcode Screen for Epigenetic Regulators Reveals a Role for the NuB4/HAT-B Histone Acetyltransferase Complex in Histone Turnover

Dynamic modification of histone proteins plays a key role in regulating gene expression. However, histones themselves can also be dynamic, which potentially affects the stability of histone modifications. To determine the molecular mechanisms of histone turnover, we developed a parallel screening method for epigenetic regulators by analyzing chromatin states on DNA barcodes. Histone turnover was quantified by employing a genetic pulse-chase technique called RITE, which was combined with chromatin immunoprecipitation and high-throughput sequencing. In this screen, the NuB4/HAT-B complex, containing the conserved type B histone acetyltransferase Hat1, was found to promote histone turnover. Unexpectedly, the three members of this complex could be functionally separated from each other as well as from the known interacting factor and histone chaperone Asf1. Thus, systematic and direct interrogation of chromatin structure on DNA barcodes can lead to the discovery of genes and pathways involved in chromatin modification and dynamics

Probabilistic Inference for Nucleosome Positioning with MNase-Based or Sonicated Short-Read Data

We describe a model-based method, PING, for predicting nucleosome positions in MNase-Seq and MNase- or sonicated-ChIP-Seq data. PING compares favorably to NPS and TemplateFilter in scalability, accuracy and robustness to low read density. To demonstrate that PING predictions from widely available sonicated data can have sufficient spatial resolution to be to be useful for biological inference, we use Illumina H3K4me1 ChIP-seq data to detect changes in nucleosome positioning around transcription factor binding sites due to tamoxifen stimulation, to discriminate functional and non-functional transcription factor binding sites more effectively than with enrichment profiles, and to confirm that the pioneer transcription factor Foxa2 associates with the accessible major groove of nucleosomal DNA

Freqüência de infecção por Toxocara em crianças atendidas em serviço público de Maringá, sul do Brasil

The lack of specific laboratorial diagnosis methods and precise symptoms makes the toxocariasis a neglected disease in Public Health Services. This study aims to determine the frequency of Toxocara spp. infection in children attended by the Health Public Service of Hospital Municipal de Maringá, South Brazil. To evaluate the association of epidemiological and clinical data, an observational and cross-section study was carried out. From 14,690 attended children/year aged from seven month to 12 years old, 450 serum samples were randomly collected from September/2004 to September/2005. A questionnaire was used to evaluate epidemiological, clinical and hematological data. An ELISA using Toxocara canis larval excretory-secretory products as antigen detected 130 (28.8%) positive sera, mainly between children from seven month to five years old (p = 0.0016). Significant correlation was observed between positive serology for Toxocara, and frequent playing in sandbox at school or daycare center (p = 0.011) and the presence of a cat at home (p = 0.056). From the families, 50% were dog owners which exposed soil backyards. Eosinophilia (p = 0.776), and signs and symptoms analyzed (fever p = 0.992, pneumonia p = 0.289, cold-like symptoms p = 0.277, cough p = 0.783, gastrointestinal problems p = 0.877, migraine p = 0.979, abdominal pain p = 0.965, joint pain p = 0.686 and skin rash p = 0.105) could not be related to the presence of anti-Toxocara antibodies. Therefore, two asthmatics children showed titles of 1:10,240 and accentuated eosinophilia (p = 0.0001). The authors emphasize the needs of prevention activities.A falta de métodos de diagnóstico laboratorial específico e sintomas específicos fazem da toxocaríase uma doença negligenciada nos serviços públicos de saúde. Este estudo teve por objetivo determinar a freqüência de infecção por Toxocara spp. em crianças atendidas no serviço público do Hospital Municipal de Maringá, sul do Brasil, e avaliar a associação com dados epidemiológicos e clínicos, em estudo observacional e transversal. De 14.690 crianças/ano atendidas, com idade entre sete meses a 12 anos, foram coletados 450 soros de setembro/2004 a setembro/2005. Um questionário foi utilizado para avaliar dados epidemiológicos, clínicos e hematológicos. Pelo teste ELISA, com antígeno de excreção/secreção de larvas de Toxocara canis, detectou-se 130 (28,8%) soros positivos, principalmente em crianças entre sete meses e cinco anos (p = 0,0016). Houve significante correlação entre sorologia positiva para Toxocara e freqüente recreação das crianças em caixas de areia da escola ou pré escola (p = 0,011) e presença do gato no domicilio (p = 0,056). Das famílias dessas crianças, 50% possuíam cachorros e o quintal com solo exposto. Eosinofilia (p = 0,776), sinais e sintomas (febre p = 0,992, pneumonia p = 0,289, resfriado p = 0,277, tosse p = 0,783, problema gastrointestinal p = 0877, dor de cabeça p = 0,979, dor abdominal p = 0,965, dores articulares p = 0,686, urticária p = 0,105) não se correlacionaram com a soropositividade. Todavia, duas crianças asmáticas apresentaram títulos de 1:10.240 (>; 1:320) e acentuada eosinofilia (p = 0.0001). Os autores enfatizam a necessidade de atividades preventivas

SOS Response Induces Persistence to Fluoroquinolones in Escherichia coli

Bacteria can survive antibiotic treatment without acquiring heritable antibiotic resistance. We investigated persistence to the fluoroquinolone ciprofloxacin in Escherichia coli. Our data show that a majority of persisters to ciprofloxacin were formed upon exposure to the antibiotic, in a manner dependent on the SOS gene network. These findings reveal an active and inducible mechanism of persister formation mediated by the SOS response, challenging the prevailing view that persisters are pre-existing and formed purely by stochastic means. SOS-induced persistence is a novel mechanism by which cells can counteract DNA damage and promote survival to fluoroquinolones. This unique survival mechanism may be an important factor influencing the outcome of antibiotic therapy in vivo

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field

Frequency of eosinophilia and risk factors and their association with Toxocara infection in schoolchildren during a health survey in the north of Lima, Peru

During a health survey in a primary school from the district of Carabayllo (North of Lima, Peru), 200 schoolchildren (96 male and 104 female between five to 12 years old) were randomly selected and divided in two groups (as positive or negative group), according to the serologic result of the Toxocara ELISA test from a total population of 646 schoolchildren. All children were analyzed by hematologic tests to determinate the frequency of eosinophilia and leukocytosis. Additionally, all clinical and epidemiological data were also analyzed to determine their association with toxocariasis. From group of children with positive serology, 40% had some type of eosinophilia in contrast to 19% of children with negative serology, and their association was statistically significant (OR = 2.84, p < 0.001). From all signs and symptoms evaluated, only 'dry cough' was more frequent and statistically significant in the positive serology group (OR = 2.79, p < 0.001). Almost all risk factors evaluated were highly frequent and statistically associated to the positive serology. In conclusion, the presence of eosinophilia and the risk factors evaluated in this population were frequently associated to human toxocariasis

Induction of a stable, heritable epigenetic change by mutagenic carcinogens: A new test system

SCOPUS: ar.jinfo:eu-repo/semantics/publishe

A system for detection of genetic and epigenetic alterations in Escherichia coli induced by DNA-damaging agents

SCOPUS: ar.jinfo:eu-repo/semantics/publishe