Nuclease Digestion Research Articles

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide-encoding genes in vertebrates, providing an entry point to define their function in vivo.

Sodium butyrate remodels whole genome nucleosome maps and attenuates high fat diet‐induced mitochondrial dysfunction in skeletal muscle from C57BL6/J mice (1072.1)

High fat diets (HFDs) largely contribute to the onset and progression of obesity and type 2 diabetes and are used to generate models of diet‐induced obesity and insulin resistance; yet, the epigenetic mechanisms underlying the effects of HFDs are not fully understood. Here, we determined whole genome differences in nucleosome occupancy or positioning in skeletal muscle from C57BL6/J mice fed either a 10% low fat diet (LFD), 60% HFD or 60% HFD plus sodium butyrate (NaB) for 9wks using microccocal nuclease digestion followed by high throughput sequencing (MNase‐seq). Additionally, metabolomics of 45 various acylcarnitine species and ratios and immunohistochemistry for fiber typing were performed in the quadriceps muscle. We show that NaB supplementation prevents HFD‐induced obesity and insulin resistance and that diet‐induced changes in nucleosome occupancy and positioning are associated with parallel increases in muscle mitochondrial function and type 1 oxidative fiber content. Targeted analysis of peroxisome proliferator‐activated receptor gamma coactivator 1 alpha (Pgc1α), also suggests that ‐1 nucleosome positioning within the Pgc1α promoter may be important in diet‐induced mitochondrial adaptation. These data provide additional identified genomic loci that may be epigenetically regulated by diet to determine skeletal muscle mitochondrial adaptation.Grant Funding Source: Supported by NIH NIDDK 5T32‐DK064584‐09 (TMH), NIH COBRE 8P20‐GM103528‐07 and NORC 5P30‐DK072476‐07

The Tripartite Virions of the Brome Mosaic Virus Have Distinct Physical Properties That Affect the Timing of the Infection Process

The three subsets of virions that comprise the Brome mosaic virus (BMV) were previously thought to be indistinguishable. This work tested the hypothesis that distinct capsid-RNA interactions in the BMV virions allow different rates of viral RNA release. Several results support distinct interactions between the capsid and the BMV genomic RNAs. First, the deletion of the first eight residues of the BMV coat protein (CP) resulted in the RNA1-containing particles having altered morphologies, while those containing RNA2 were unaffected. Second, subsets of the BMV particles separated by density gradients into a pool enriched for RNA1 (B1) and for RNA2 and RNA3/4 (B2.3/4) were found to have different physiochemical properties. Compared to the B2.3/4 particles, the B1 particles were more sensitive to protease digestion and had greater resistivity to nanoindentation by atomic force microscopy and increased susceptibility to nuclease digestion. Mapping studies showed that portions of the arginine-rich N-terminal tail of the CP could interact with RNA1. Mutational analysis in the putative RNA1-contacting residues severely reduced encapsidation of BMV RNA1 without affecting the encapsidation of RNA2. Finally, during infection of plants, the more easily released RNA1 accumulated to higher levels early in the infection. Viruses with genomes packaged in distinct virions could theoretically release the genomes at different times to regulate the timing of gene expression. Using an RNA virus composed of three particles, we demonstrated that the RNA in one of the virions is released more easily than the other two in vitro. The differential RNA release is due to distinct interactions between the viral capsid protein and the RNAs. The ease of RNA release is also correlated with the more rapid accumulation of that RNA in infected plants. Our study identified a novel role for capsid-RNA interactions in the regulation of a viral infection.

Interference of Co-Amplified Nuclear Mitochondrial DNA Sequences on the Determination of Human mtDNA Heteroplasmy by Using the SURVEYOR Nuclease and the WAVE HS System

High-sensitivity and high-throughput mutation detection techniques are useful for screening the homoplasmy or heteroplasmy status of mitochondrial DNA (mtDNA), but might be susceptible to interference from nuclear mitochondrial DNA sequences (NUMTs) co-amplified during polymerase chain reaction (PCR). In this study, we first evaluated the platform of SURVEYOR Nuclease digestion of heteroduplexed DNA followed by the detection of cleaved DNA by using the WAVE HS System (SN/WAVE-HS) for detecting human mtDNA variants and found that its performance was slightly better than that of denaturing high-performance liquid chromatography (DHPLC). The potential interference from co-amplified NUMTs on screening mtDNA heteroplasmy when using these 2 highly sensitive techniques was further examined by using 2 published primer sets containing a total of 65 primer pairs, which were originally designed to be used with one of the 2 techniques. We confirmed that 24 primer pairs could amplify NUMTs by conducting bioinformatic analysis and PCR with the DNA from 143B-ρ0 cells. Using mtDNA extracted from the mitochondria of human 143B cells and a cybrid line with the nuclear background of 143B-ρ0 cells, we demonstrated that NUMTs could affect the patterns of chromatograms for cell DNA during SN-WAVE/HS analysis of mtDNA, leading to incorrect judgment of mtDNA homoplasmy or heteroplasmy status. However, we observed such interference only in 2 of 24 primer pairs selected, and did not observe such effects during DHPLC analysis. These results indicate that NUMTs can affect the screening of low-level mtDNA variants, but it might not be predicted by bioinformatic analysis or the amplification of DNA from 143B-ρ0 cells. Therefore, using purified mtDNA from cultured cells with proven purity to evaluate the effects of NUMTs from a primer pair on mtDNA detection by using PCR-based high-sensitivity methods prior to the use of a primer pair in real studies would be a more practical strategy.

P19INK4d is involved in the cellular senescence mechanism contributing to heterochromatin formation

BackgroundDuring evolution, organisms with renewable tissues have developed mechanisms to prevent tumorigenesis, including cellular senescence and apoptosis. Cellular senescence is characterized by a permanent cell cycle arrest triggered by both endogenous stress and exogenous stress. The p19INK4d, a member of the family of cyclin-dependent kinase inhibitors (INK4), plays an important role on cell cycle regulation and in the cellular DNA damage response. We hypothesize that p19INK4d is a potential factor involved in the onset and/or maintenance of the senescent state. MethodsSenescence was confirmed by measuring the cell cycle arrest and the senescence-associated β-galactosidase activity. Changes in p19INK4d expression and localization during senescence were determined by Western blot and immunofluorescence assays. Chromatin condensation was measured by microccocal nuclease digestion and histone salt extraction. ResultsThe data presented here show for the first time that p19INK4d expression is up-regulated by different types of senescence. Changes in senescence-associated hallmarks were driven by modulation of p19 expression indicating a direct link between p19INK4d induction and the establishment of cellular senescence. Following a senescence stimulus, p19INK4d translocates to the nucleus and tightly associates with chromatin. Moreover, reduced levels of p19INK4d impair senescence-related global genomic heterochromatinization. Analysis of p19INK4d mRNA and protein levels in tissues from differently aged mice revealed an up-regulation of p19INK4d that correlates with age. ConclusionWe propose that p19INK4d participates in the cellular mechanisms that trigger senescence by contributing to chromatin compaction. General significanceThis study provides novel insights into the dynamics process of cellular senescence, a central tumor suppressive mechanism.

Assay of methylglyoxal-derived protein and nucleotide AGEs

Glyoxalase- and methylglyoxal-related research has required the development of quantitative and reliable techniques for the measurement of methylglyoxal-derived glycation adducts of protein and DNA. There are also other glycation adducts, oxidation adducts and nitration adducts of proteins and oxidation adducts of DNA. Proteolysis of protein releases glycation, oxidation and nitration free adducts (glycated, oxidized and nitrated amino acids) in plasma and nuclease digestion of DNA releases glycated and oxidized nucleosides into plasma and other body fluids for excretion in urine. The gold standard method for quantifying these adducts is stable isotopic dilution analysis LC-MS/MS. Protein and DNA adduct residues are determined by assay of enzymatic hydrolysates of protein and DNA extracts prepared using cocktails of proteases and nucleases respectively. Free adducts are determined by analysis of ultrafiltrates of plasma, urine and other physiological fluids. Protein damage markers (13 glycation adducts, five oxidation adducts and 3-nitrotyrosine) and DNA damage markers (three glycation adducts and one oxidation adduct) are quantified using 25 μg of protein, 10 μg of DNA or 5 μl of physiological fluid. Protein and nucleotide AGE (advanced glycation end-product) assay protocols resistant to interferences is described.

Chromatin remodelling complex RSC promotes base excision repair in chromatin of Saccharomyces cerevisiae

The base excision repair (BER) pathway is a conserved DNA repair system required to maintain genomic integrity and prevent mutagenesis in all eukaryotic cells. Nevertheless, how BER operates in vivo (i.e. in the context of chromatin) is poorly understood. We have investigated the role of an essential ATP-dependent chromatin remodelling (ACR) complex RSC (Remodels the Structure of Chromatin) in BER of intact yeast cells. We show that depletion of STH1, the ATPase subunit of RSC, causes enhanced sensitivity to the DNA alkylating agent methyl methanesulfonate (MMS) and results in a substantial inhibition of BER, at the GAL1 locus and in the genome overall. Consistent with this observation, the DNA in chromatin is less accessible to micrococcal nuclease digestion in the absence of RSC. Quantitative PCR results indicate that repair deficiency in STH1 depleted cells is not due to changes in the expression of BER genes. Collectively, our data indicates the RSC complex promotes efficient BER in chromatin. These results provide, for the first time, a link between ATP-dependent chromatin remodelling and BER in living cells.

Histone H3 phosphorylation near the nucleosome dyad alters chromatin structure

Nucleosomes contain ∼146 bp of DNA wrapped around a histone protein octamer that controls DNA accessibility to transcription and repair complexes. Posttranslational modification (PTM) of histone proteins regulates nucleosome function. To date, only modest changes in nucleosome structure have been directly attributed to histone PTMs. Histone residue H3(T118) is located near the nucleosome dyad and can be phosphorylated. This PTM destabilizes nucleosomes and is implicated in the regulation of transcription and repair. Here, we report gel electrophoretic mobility, sucrose gradient sedimentation, thermal disassembly, micrococcal nuclease digestion and atomic force microscopy measurements of two DNA–histone complexes that are structurally distinct from nucleosomes. We find that H3(T118ph) facilitates the formation of a nucleosome duplex with two DNA molecules wrapped around two histone octamers, and an altosome complex that contains one DNA molecule wrapped around two histone octamers. The nucleosome duplex complex forms within short ∼150 bp DNA molecules, whereas altosomes require at least ∼250 bp of DNA and form repeatedly along 3000 bp DNA molecules. These results are the first report of a histone PTM significantly altering the nucleosome structure.

Transcription of theGeminingene is regulated by a negative-feedback loop

Geminin performs a central function in regulating cellular proliferation and differentiation in development and also in stem cells. Of interest, down-regulation of Geminin induces gene transcription regulated by E2F, indicating that Geminin is involved in regulation of E2F-mediated transcriptional activity. Because transcription of the Geminin gene is reportedly regulated via an E2F-responsive region (E2F-R) located in the first intron, we first used a reporter vector to examine the effect of Geminin on E2F-mediated transcriptional regulation. We found that Geminin transfection suppressed E2F1- and E2F2-mediated transcriptional activation and also mildly suppressed such activity in synergy with E2F5, 6, and 7, suggesting that Geminin constitutes a negative-feedback loop for the Geminin promoter. Of interest, Geminin also suppressed nuclease accessibility, acetylation of histone H3, and trimethylation of histone H3 at lysine 4, which were induced by E2F1 overexpression, and enhanced tri-methylation of histone H3 at lysine 27 and monoubiquitination of histone H2A at lysine 119 in E2F-R. However, Geminin5EQ, which does not interact with Brahma or Brg1, did not suppress accessibility to nuclease digestion or transcription but had an overall dominant-negative effect. These findings suggest that E2F-mediated activation of Geminin transcription is negatively regulated by Geminin through the inhibition of chromatin remodeling.

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

All eukaryotic cells divide a finite number of times, although the mechanistic basis of this replicative aging remains unclear. Replicative aging is accompanied by a reduction in histone protein levels, and this is a cause of aging in budding yeast. Here we show that nucleosome occupancy decreased by 50% across the whole genome during replicative aging using spike-in controlled micrococcal nuclease digestion followed by sequencing. Furthermore, nucleosomes became less well positioned or moved to sequences predicted to better accommodate histone octamers. The loss of histones during aging led to transcriptional induction of all yeast genes. Genes that are normally repressed by promoter nucleosomes were most induced, accompanied by preferential nucleosome loss from their promoters. We also found elevated levels of DNA strand breaks, mitochondrial DNA transfer to the nuclear genome, large-scale chromosomal alterations, translocations, and retrotransposition during aging.

Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes

Excision of introns from pre-mRNAs is mediated by the spliceosome, a multi-megadalton complex consisting of U1, U2, U4/U6, and U5 snRNPs plus scores of associated proteins. Spliceosome assembly and disassembly are highly dynamic processes involving multiple stable intermediates. In this study, we utilized a split TAP-tag approach for large-scale purification of an abundant endogenous U2·U5·U6 complex from Schizosaccharomyces pombe. RNAseq revealed this complex to largely contain excised introns, indicating that it is primarily ILS (intron lariat spliceosome) complexes. These endogenous ILS complexes are remarkably resistant to both high-salt and nuclease digestion. Mass spectrometry analysis identified 68, 45, and 43 proteins in low-salt-, high-salt-, and micrococcal nuclease-treated preps, respectively. The protein content of a S. pombe ILS complex strongly resembles that previously reported for human spliced product (P) and Saccharomyces cerevisiae ILS complexes assembled on single pre-mRNAs in vitro. However, the ATP-dependent RNA helicase Brr2 was either substoichiometric in low-salt preps or completely absent from high-salt and MNase preps. Because Brr2 facilitates spliceosome disassembly, its relative absence may explain why the ILS complex accumulates logarithmically growing cultures and the inability of S. pombe extracts to support in vitro splicing.

On-Chip Analysis of Intermittent Molecular Encounters in Nuclease Digestion of Specific DNA Sequence

DNA-binding proteins such as transcription factors react with their targets at faster than estimation from diffusion-controlled rates. This is explained by the fact that the protein can slide along DNA molecule with appreciable affinity for nonspecific sequences. However, does this sliding function really play a key role in this type of reaction kinetics? Most of the previous methods are optimized for one-dimensional protein diffusion along DNA maintained in an extended configuration. Here we show that a site-specific nuclease digestion efficiently occurs in the course of an intermittent encounter by the same single DNA molecule to a number of nucleolytic enzyme molecules. We found in a limited protein's sliding-free condition that the intermittent molecular encounter and complex formation process gives an enhanced rate for the reaction. Our results demonstrate how the flowing DNA encounters the immobilized restriction enzyme ApaI by which the site-specific DNA-break occurs. Moving tags of both DNA ends transmitted the breakup of single DNA molecule into fragments. Quite a number of digestions occurred at the first encounter (62%), but the remaining 38% of digestion occurred in the course of the subsequent intermittent encounters. The complex formation was maintained after the DNA break. This is suggestive of an intrinsic behaviour in which the DNA and protein molecules are continuously held together by switching their binding positions with short-range interactions. It also provides a clue to understanding an efficient and effective reaction by the DNA-binding proteins in bacterial cells.

Triazole-linked analogues of DNA and RNA ((TL)DNA and (TL)RNA): synthesis and functions.

Click chemistry has provided us with access to DNA and RNA analogues with non-natural triazole internucleoside linkages. The bond periodicity of the oligonucleotides was designed to enforce duplex formation with natural congeners, and the non-cleavable linkages protect the oligomers against nuclease digestion. This account reviews the progress of the triazole-linked analogues over the past five years. Reinforced by their synthetic robustness, these analogues may find various utilities as tools for exploratory research.

Regulation Of Normal and Malignant Hoxa Gene Expression Through Higher H3K79 Methylated States

The clustered Hoxa genes Hoxa5-Hoxa10 are important for self-renewal and differentiation of hematopoietic stem and progenitor cells. These genes are often aberrant upregulated in human malignancies, one of the most striking examples of which are leukemias with rearrangements of the mixed lineage leukemia (MLL) gene. Since these key posterior Hoxa cluster genes are known to show graded down-regulation upon hematopoietic differentiation, we sought to assess the epigenetic changes associated with this tightly controlled, developmentally critical transcriptional program. We performed ChIP sequencing on lineage negative, Sca-1 + Kit + (LSK) cells where the posterior Hoxa5-10genes are highly expressed compared to granulocyte macrophage progenitors (GMPs) that show markedly lower expression of these transcripts. We observed a dramatic diminution in H3K79 di/tri methylation as cells differentiated from LSKs to GMPs. In contrast, we found minimal changes in H3K79 mono-methylation during the LSK-GMP transition suggesting that high expression of Hoxa genes is maintained through higher H3K79 methylated states in normal hematopoiesis. Strikingly, the removal of H3K79 me2/3 but not me1 was sufficient for repressive epigenetic mechanisms such as polycomb repressive complex 2 (PRC2)- mediated H3K27 tri-methylation to invade the Hoxa locus during the LSK to GMP differentiation. The decrease in H3K79 di/tri methylation upon hematopoietic differentiation may be the result of a graded decrease in expression of the DOT1L co-factor Af10 which we have recently found to regulate the transition from H3K79 mono to dimethylation.Next we wanted to probe whether MLL-leukemias drive Hoxa gene expression through increased conversion of H3K79 methylation from the mono to the di/tri-methylated states. We performed ChIP sequencing for H3K79 me1/2/3 to identify the different states of H3K79 methylation across the epigenetic landscape of MLL-transformed cells. Strikingly we observed that in both murine and human leukemia, there was a dramatic hyper-conversion of H3K79 mono-methylation to di/trimethylation specifically at MLL-AF9 target genes. Af10 deletion in the MLL-AF9 leukemia significantly reduced H3K79me2/3 while retaining - and in some cases even increasing - H3K79 me1 at MLL-target genes. We then assessed chromatin accessibility at the Hoxa locus following nuclease digestion and observed that the diminution of H3K79me2/3 was enough to significantly reduce chromatin accessibility at the Hoxa locus despite the relative retention of H3K79me1. Similar to the LSK-GMP transition, reduction in H3K79 me2/3 but not H3K79me1 was accompanied by a dramatic increase in H3K27me3 in a very specific subset of genes including Hoxa5-10.The genetic and epigenetic changes resulting from Af10 deletion significantly impaired MLL-leukemogenesis and sensitized leukemia cells to DOT1L inhibition. These results suggest that the expression of Hoxa genes in hematopoiesis is controlled through higher H3K79 methylated states, possibly aided by the DOT1L co-factor Af10. The MLL-AF9 fusion seems to hijack this mode of regulation through aberrant hyperconversion of H3K79 methylation to higher methylated states at critical oncogenic targets including the Hoxa genes. These data suggest that targeting the interaction between DOT1L and Af10 is a potential therapeutic strategy since it blunts the conversion of H3K79me1 to higher states of methylation by MLL-fusion proteins and thus significantly impairs MLL-mediated transformation. Disclosures:Armstrong:Epizyme: Consultancy.

Characterization Of Chromatin Dynamics In Mammalian Erythropoiesis

Mammalian erythropoiesis is a dynamic process in which erythroid progenitors proliferate and differentiate into mature enucleated red blood cells. In the late stage of erythropoiesis, erythroblasts undergo terminal cell-cycle exit, chromatin condensation and extrusion of the pycnotic nucleus via an asymmetric cell division. Recent genetic and biochemical studies illustrated that various signaling pathways, including histone deacetylations and other chromatin modifications, are involved in chromatin condensation and enucleation. However, it is unclear the global dynamic changes of the nucleosome and how different histones are regulated during chromatin condensation.We proposed to directly characterize the expression levels and localization of different histones and their variants during erythropoiesis. We found that histone H2A and its variants are differentially expressed during erythropoieisis, while the levels of other histones including H2B, histone H3 and histone H4 remained unchanged. To determine their localization, we performed immunofluorescence experiments of these histones together with nuclear lamins. Strikingly, lamin B staining revealed a gradually enlarged nuclear opening through which most histones, except histone H2AZ, were released out of the nucleus. This nuclear opening was confirmed by electron microscopy. The same phenotype was observed in vivo in freshly purified late stage erythroblasts. Western blot analysis confirmed this release, however, many well known nuclear proteins remained in the nucleus in this process. Mechanistically, we demonstrated that caspase 3 was involved in the regulation of nuclear openings during erythropoieiss. Inhibition or knockdown of caspase 3 completely blocked lamin B opening and histone release, which led to inhibition of chromatin condensation and cell differentiation, and ultimate cell death.In summary, our study demonstrated that the dynamic changes of various histones, with their selective and gradual release out of the nucleus, is required for chromatin condensation and differentiation during erythropoieisis. Studies of the detailed mechanisms are ongoing. Particularly, we are using micrococcal nuclease digestion of chromatin followed by next generation sequencing technology (MNase-seq) to determine genome-wide nucleosome location during the differention. Chromatin- immunoprecipitation (ChIP) will also be performed to determine H2A family protein locations during erythropoiesis. Disclosures:No relevant conflicts of interest to declare.

NucVoter: A Voting Algorithm for Reliable Nucleosome Prediction Using Next-Generation Sequencing Data.

Nucleosomes, which consist of DNA wrapped around histone octamers, are dynamic, and their structure, including their location, size, and occupancy, can be transformed. Nucleosomes can regulate gene expression by controlling the DNA accessibility of proteins. Using next-generation sequencing techniques along with such laboratory methods as micrococcal nuclease digestion, predicting the genomic locations of nucleosomes is possible. However, the true locations of nucleosomes are unknown, and it is difficult to determine their exact locations using next-generation sequencing data. This paper proposes a novel voting algorithm, NucVoter, for the reliable prediction of nucleosome locations. Multiple models verify the consensus areas in which nucleosomes are placed by the model with the highest priority. NucVoter significantly improves the performance of nucleosome prediction.

Glycosylated Liposomes with Proton Sponge Capacity: Novel Hepatocyte- Specific Gene Carriers

Interest in hepatocyte-directed liposomal gene delivery is driven, in part, by the lack of effective treatment for several liver-associated disorders. To impart a hepatocyte targeting capability on DNA-lipoplexes, and to promote early release of cargo DNA from endosomes, novel glycosylated and imidazolylated cholesteryl derivatives have been synthesized and evaluated in vitro. Thus cholesteryl-3β-N-[(lactobionyl) amino] carbamate (Chol-LAC) and cholesteryl-3β-N- [(urocanyl) amino] carbamate (Chol-UAC) have been formulated with the cytofectin cholesteryl-3β-[(N',N'- dimethylaminopropyl) carbamate (Chol-T) and the neutral co-lipid dioleoylphosphatidyl ethanolamine (DOPE). Liposomes, which displayed a buffering capability at endosomal pH, effectively bound DNA at a N/P ratio of 0.8:1 and offered partial protection against serum nuclease digestion. The MTT cell viability assay showed that lipoplexes were well tolerated by human hepatoma cells (HepG2), which were efficiently transfected almost exclusively by asialoglycoprotein receptor (ASGP-R)-mediation, as demonstrated in competition assays. In the ASGP-R-negative human kidney cell line (HEK293) transfection levels were considerably lower (P < 0.001). Therefore the combination of Chol-LAC and Chol- UAC in cationic liposomal formulations may provide a platform for the development of useful hepatotropic gene delivery systems.

Acquired carbapenemases in Enterobactericeae in Singapore, 1996-2012

To characterise carbapenemase-producing Enterobacteriaceae (CRE) isolated in Singapore. Carbapenemase genes and their flanking regions were amplified and sequenced by PCR. Isolates were typed by pulsed-field gel electrophoresis and multi-locus sequence typing. Plasmids bearing carbapenemase genes were sized by S1 nuclease digestion, Southern blotting, and DNA hybridisation with appropriate probes. Transfer of these plasmids was attempted by conjugation and transformation. Successfully transferred plasmids were characterised by polymerase chain reaction (PCR) replicon typing and restriction digestion. Isolates of Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae and Citrobacter species carried a variety of carbapenemase genes including blaIMP-1, blaIMP-4, blaNDM-1, blaNDM-7, blaOXA-181, blaOXA-48 and blaKPC-2. Apart from K. pneumoniae with blaOXA-181, and some K. pneumoniae with blaNDM-1, the other isolates were not clonal. However there appears to be some spread of plasmids with blaIMP-1, blaNDM-1,blaKPC-2, and blaOXA-48. The number of isolates of CRE has increased in Singapore, especially since 2010. There is a diversity of carbapenemase types that reflects the geographical proximity of other countries with CRE.

Comparison of the Isw1a, Isw1b, and Isw2 Nucleosome Disrupting Activities

The three Saccharomyces cerevisiae ISWI chromatin remodeling complexes, Isw1a, Isw1b, and Isw2, are implicated in the regularization of arrayed nucleosomes and regulation of gene activity. Although Isw1a and Isw1b are based on the same catalytic unit, in general, their functions in vivo do not overlap. To better understand the structural consequences of these complexes, we compared the putative nucleosome disrupting activities of the purified Isw1a, Isw1b, and Isw2. To account for the putative effects of nucleosomal environment, we employed reconstituted dinucleosomes in which the histone octamers were specifically positioned by the 146 base pair high-affinity nucleosome sequence "601". We have compared the MNase and deoxyribonuclease I protection patterns of remodeled nucleosome templates and evaluated the nucleosome destabilizing abilities of the Isw1a/b and Isw2 using restriction endonucleases. Although the Isw2 showed little evidence of nucleosome disassembly, the Isw1b remodeled dinucleosomes exhibited some common features with the ySwi-Snf remodeling products. The nuclease digestion data suggest that Isw1a can also promote ATP-dependent distortion of nucleosome structure, although less efficiently than the Isw1b complex.

Evaluation of Chitosan-Tripolyphosphate Nanoparticles as a p-shRNA Delivery Vector: Formulation, Optimization and Cellular Uptake Study

Polysaccharides (especially chitosan) have recently attracted much attention as gene therapy delivery vehicles for their unique properties such as biocompatibility, biodegradability, low toxicity, and controlled release. Nanoparticles have strong potential as a carrier of plasmid short hairpin RNA (p-shRNA). This study aimed to find the optimum conditions for obtaining Chitosan/triphosphate (TPP)/p-shRNA nanoparticles by the ionic gelation method, and investigating the cellular uptake of the optimized nanoparticles. After applying the central composite design of response surface methodology (RSM), the optimum conditions for preparation of nanoparticles with small size and high loading efficiency were: chitosan/TPP ratio = 10, pH = 5.5 and N/P ratio = 11. The resulting nanoparticles had an average size of 172.8 ± 7 nm and loading efficiency of 71.5 ± 5%. SEM images showed spherical and smooth nanoparticles. The nanoparticles complexed with p-shRNA and may protect it against nuclease digestion. Cytotoxicity studies with HeLa and PC3 human cancer cells demonstrated that chitosan/TPP nanoparticles had low toxicity. Cellular uptake studies using HeLa cells showed that the nanoparticles entered the cells (cellular uptake) and delivered DNA, probably due to their favorable Zeta potential (approximately +28 mV) and small size.