Intrapleural tissue plasminogen activator (tPA) and deoxyribonuclease (DNase) therapy is being increasingly employed as an alternative to surgical intervention for the treatment of complicated parapneumonic effusions and empyema. Published cases are limited to one randomized control trial and few case reports. No data exist on employing sequential or repeated courses of intrapleural tPA/DNase t...

Chromatin fragments released from intact Friend erythroleukemia cell nuclei during limited incubation with micrococcal nuclease, DNase II or DNase I were analyzed to determine the distribution of DNA methyltransferase in chromatin. The enzyme was released in a free form when internucleosomal DNA was digested with micrococcal nuclease but was found associated with Mg++-precipitable polynucleosom...

A systematic search was performed for DNA-binding sequences of YgiP, an uncharacterized transcription factor of Escherichia coli, by using the Genomic SELEX. A total of 688 YgiP-binding loci were identified after genome-wide profiling of SELEX fragments with a high-density microarray (SELEX-chip). Gel shift and DNase-I footprinting assays indicated that YgiP binds to multiple sites along DNA pr...

Indian Echis carinatus bite causes sustained tissue destruction at the bite site. Neutrophils, the major leukocytes in the early defence process, accumulate at the bite site. Here we show that E. carinatus venom induces neutrophil extracellular trap (NET) formation. The NETs block the blood vessels and entrap the venom toxins at the injection site, promoting tissue destruction. The stability of...

The Kaposi's sarcoma-associated herpesvirus (KSHV) SOX protein, encoded by ORF37, promotes shutoff of host cell gene expression during lytic viral replication by dramatically impairing mRNA accumulation. SOX is the KSHV homolog of the alkaline exonuclease of other herpesviruses, which has been shown to function as a DNase involved in processing and packaging the viral genome. Although the exonu...

The DNase I sensitivity of chromosomal DNA regions carrying integrated proviral genomes of Moloney (M-MuLV) and AKR Murine Leukemia Virus (AKR-MuLV), and the cellular homologue of the mos-gene (c-mos) of Moloney Sarcoma Virus (MSV) were studied in tumor tissues of leukemic mice. The genetically transmitted sequences of M-MuLV, AKR-MuLV, and the c-mos gene are all in DNase I resistant chromatin ...

The cytolethal distending toxin B (CdtB) of the mouse pathogen Helicobacter hepaticus has cation binding and DNA catalysis residues in common with members of the mammalian deoxyribonuclease I (DNase I) family. The purpose of the present study was to characterize CdtB nuclease. To establish optimal digestion conditions and to evaluate co-factor requirements, a novel and sensitive fluorometric as...

The chromatin of the lepidopteran Ephestia kuehniella was digested by micrococcal nuclease, DNase I and S1-nuclease combined with DNase I pretreatment. The resulting DNA fragments were analyzed by gel electrophoresis and compared with the DNA fragments of rat liver nuclei obtained by the same process. Extensive homology was revealed between insect and mammalian chromatin structure. The combined...

We show that existing RNA-seq, DNase-seq, and ChIP-seq data exhibit overdispersed per-base read count distributions that are not matched to existing computational method assumptions. To compensate for this overdispersion we introduce a nonparametric and universal method for processing per-base sequencing read count data called FIXSEQ. We demonstrate that FIXSEQ substantially improves the perfor...