A SWI/SNF-like factor from chicken liver that disrupts nucleosomes and transfers histone octamers in cis and trans

ATP-dependent chromatin remodeling factors have been implicated in nuclear processes involving DNA. Here we report partial purification and characterization of an ATP-dependent chromatin remodeling activity from chicken liver. Nuclear extract from chicken liver was fractionated chromatographically to enrich proteins immunoreacting to antibodies against components of human SWI/SNF, namely BRG1, BAF170, BAF155, and BAF57. Immunoreactivity to these antibodies elutes with a mass of about 2MDa on Sepharose CL-6B gel filtration, suggesting that they constitute a SWI/SNF-like complex (SLC). The SLC displays three chromatin-remodeling activities, viz. nucleosome disruption, octamer transfer, and nucleosome sliding (octamer transfer in cis). We further show that components of SLC, as revealed by immunoreactivity to the above antibodies, display a dynamic nucleocytoplasmic distribution and colocalize with RNA polymerase II in the liver nuclei. This report contributes to the understanding of phylogenetic generality of chromatin remodeling factors in eukaryotes.     

Uridylate addition and RNA ligation contribute to the specificity of kinetoplastid insertion RNA editing

RNA editing in Trypanosoma brucei inserts and deletes uridylates (U's) in mitochondrial pre-mRNAs under the direction of guide RNAs (gRNAs). We report here the development of a novel in vitro precleaved editing assay and its use to study the gRNA specificity of the U addition and RNA ligation steps in insertion RNA editing. The 5' fragment of substrate RNA accumulated with the number of added U's specified by gRNA, and U addition products with more than the specified number of U's were rare. U addition up to the number specified occurred in the absence of ligation, but accumulation of U addition products was slowed. The 5' fragments with the correct number of added U's were preferentially ligated, apparently by adenylylated RNA ligase since exogenously added ATP was not required and since ligation was eliminated by treatment with pyrophosphate. gRNA-specified U addition was apparent in the absence of ligation when the pre-mRNA immediately upstream of the editing site was single stranded and more so when it was base paired with gRNA. These results suggest that both the U addition and RNA ligation steps contributed to the precision of RNA editing.     

Strong and weak hydrogen bonds in drug-DNA complexes: A statistical analysis

A statistical analysis of strong and weak hydrogen bonds in the minor groove of DNA was carried out for a set of 70 drug-DNA complexes. The terms ‘strong’ and ‘weak’ pertain to the inherent strengths and weakness of the donor and acceptor fragments rather than to any energy considerations. The dataset was extracted from the protein data bank (PDB). The analysis was performed with an in-house software, hydrogen bond analysis tool (HBAT). In addition to strong hydrogen bonds such as O—H⋯O and N—H⋯O, the ubiquitous presence of weak hydrogen bonds such as C—H⋯O is implicated in molecular recognition. On an average, there are 1.4 weak hydrogen bonds for every strong hydrogen bond. For both categories of interaction, the N(3) of purine and the O(2) of pyrimidine are favoured acceptors. Donor multifurcation is common with the donors generally present in the drug molecules, and shared by hydrogen bond acceptors in the minor groove. Bifurcation and trifurcation are most commonly observed. The metrics for strong hydrogen bonds are consistent with established trends. The geometries are variable for weak hydrogen bonds. A database of recognition geometries for 26 literature amidinium-based inhibitors of Human African Trypanosomes (HAT) was generated with a docking study using seven inhibitors which occur in published crystal structures included in the list of 70 complexes mentioned above, and 19 inhibitors for which the drug-DNA complex crystal structures are unknown. The virtual geometries so generated correlate well with published activities for these 26 inhibitors, justifying our assumption that strong and weak hydrogen bonds are optimized in the active site.     

Molecular interplay of autophagy and endocytosis in human health and diseases

Autophagy, an evolutionarily conserved process for maintaining the physio‐metabolic equilibrium of cells, shares many common effector proteins with endocytosis. For example, tethering proteins involved in fusion like Ras‐like GTPases (Rabs), soluble N‐ethylmaleimide sensitive factor attachment protein receptors (SNAREs), lysosomal‐associated membrane protein (LAMP), and endosomal sorting complex required for transport (ESCRT) have a dual role in endocytosis and autophagy, and the trafficking routes of these processes converge at lysosomes. These common effectors indicate an association between budding and fusion of membrane‐bound vesicles that may have a substantial role in autophagic lysosome reformation, by sensing cellular stress levels. Therefore, autophagy–endocytosis crosstalk may be significant and implicates a novel endocytic regulatory pathway of autophagy. Moreover, endocytosis has a pivotal role in the intake of signalling molecules, which in turn activates cascades that can result in pathophysiological conditions. This review discusses the basic mechanisms of this crosstalk and its implications in order to identify potential novel therapeutic targets for various human diseases.     

Co-Carriage of bla KPC-2 and bla NDM-1 in Clinical Isolates of Pseudomonas aeruginosa Associated with Hospital Infections from India

Global spread of KPC poses to be a serious threat complicating treatment options in hospital settings. The present study investigates the genetic environment of bla _KPC-2 among clinical isolates of Pseudomonas aeruginosa from a tertiary referral hospital of India. The study isolates were collected from different wards and clinics of Silchar Medical College and Hospital, India, from 2012–2013. The presence of bla _KPC was confirmed by genotypic characterization followed by sequencing. Cloning of the bla _KPC-2 gene was performed and the genetic environment of this gene was characterized as well. Transferability of the resistance gene was determined by transformation assay and Southern hybridization. Additionally, restriction mapping was also carried out. Two isolates of P. aeruginosa were found to harbor bla _KPC-2, were resistant towards aminoglycosides, quinolone and β-lactam-β-lactamase inhibitor combination. In both the isolates, the resistance determinant was associated with class 1 integron and horizontally transferable. Both the isolates were co-harboring bla _NDM-1. The first detection of this integron mediated bla _KPC-2 coexisting with bla _NDM-1 in P. aeruginosa from India is worrisome, and further investigation is required to track the gene cassette mediated bla _KPC-2 in terms of infection control and to prevent the spread of this gene in hospitals as well as in the community.     

Good Thinking or Gut Feeling? Cognitive Reflection and Intuition in Traders,Bankers and Financial Non-Experts

The current study investigated differences in decision-making style and risk-taking between financial traders, non-trading bank employees, and people not working in finance. Traders scored significantly higher than participants in the other two groups on the cognitive reflection test (CRT) which measures the tendency to inhibit automatic but frequently false responses in reasoning tasks. Scores for traders compared to people outside the banking sector were also higher on a self-rated scale for reflective thinking in decision-making, but there were no differences in self-rated intuitive thinking between groups. Financial risk-taking correlated with cognitive reflection scores and was significantly lower in the non-expert group compared to the other groups working in financial services. Traders in the current study showed no elevated preference to use ‘intuition’ in their decision-making compared to other groups. Overall, these results indicate that compared to non-expert participants financial traders have a higher self-rated tendency for reflective thinking and a greater propensity to inhibit the use of mental shortcuts (heuristics) in decision-making.     

Anthropogenic impact on water quality of Chilika lagoon RAMSAR site: a statistical approach

This paper investigated the spatio-temporal variability of water quality parameters (transparency, salinity, dissolved oxygen, nutrients viz. NH₃-N, NO₂-N, NO₃⁻-N, PO₄³-P, total nitrogen, total phosphorous and chlorophyll-a) in Chilika lagoon during 2001–2003 in order to better understand its ecological characteristics. Marked spatial and seasonal variations were detected with respect to almost all parameters studied. Northern sector of the lagoon is more affected by the anthropogenic stress from the catchments than the southern sector. Addition of nitrogen and phosphorous compounds to the lagoon mainly occurred through the drainage from agricultural lands and river run off during the early months of paddy cultivating seasons. Phytoplankton productivity of the lagoon was nitrogen limited, as suggested by nitrogen to phosphorous ratio. Processes affecting the water quality of the lagoon system included agricultural drainage, sewage intrusion, macrophyte litter fall and exchange of water between lagoon and the sea (Bay of Bengal). Further in depth study pertaining to quantification of exogenous material input and their disposal is recommended to ensure proper management of the lagoon and its resources.     

The capsule polysaccharide structure and biogenesis for non-O1 Vibrio cholerae NRT36S: genes are embedded in the LPS region

Background  

In V. cholerae, the biogenesis of capsule polysaccharide is poorly understood. The elucidation of capsule structure and biogenesis is critical to understanding the evolution of surface polysaccharide and the internal relationship between the capsule and LPS in this species. V. cholerae serogroup O31 NRT36S, a human pathogen that produces a heat-stable enterotoxin (NAG-ST), is encapsulated. Here, we report the covalent structure and studies of the biogenesis of the capsule in V. cholerae NRT36S.     

The effect of pH and organic ester penetration enhancers on skin permeation kinetics of terbutaline sulfate from pseudolatex-type transdermal delivery systems through mouse and human cadaver skins

The purpose of this research was to prepare a pseudolatex transdermal delivery system for terbutaline sulfate and to evaluate the effect of pH and organic ester penetration enhancers on permeation kinetics of terbutaline sulfate through mice abdominal skin and human cadaver skin. An increase in the permeation flux by increasing pH was observed. The distribution coefficient of terbutaline sulfate between 1-octanol and buffers of different pH values was also pH-dependent. Furthermore, the change of the permeability coefficient with pH correlated well with the distribution coefficient by a 2-degree polynomial equation. The permeation profile and related kinetic parameters of terbutaline sulfate was determined in presence of 3 estertype permeation enhancers incorporated in the films, viz methyl laureate, isopropyl lanolate, and isopropyl myristate. Among the 3, the more pronounced enhancing effect was obtained with isopropyl myristate, regarding the permeatin flux, permeability coefficient, and diffusion coefficient. This was attributed to solubility parameter of isopropyl myristate being closer to the solubility parameter of human skin, and such a pronounced enhancing effect was probably caused by its passage across the skin barrier through the lipid pathway. Published: September 30, 2005