Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors

Background  

The tear film is a thin layer of fluid that covers the ocular surface and is involved in lubrication and protection of the eye. Little is known about the protein composition of tear fluid but its deregulation is associated with disease states, such as diabetic dry eyes. This makes this body fluid an interesting candidate for in-depth proteomic analysis.     

Solid-phase synthesis of acridine-based threading intercalator peptides

The preparation of a novel acridine-based amino acid is reported. This N-Alloc-protected monomer can be coupled and deprotected under solid-phase peptide synthesis procedures to create acridine peptide conjugates as potential threading intercalators. A peptide containing this novel amino acid undergoes spectral changes in the presence of duplex DNA and RNA consistent with intercalative binding.     

Nucleoside analog studies indicate mechanistic differences between RNA-editing adenosine deaminases

Adenosine deaminases acting on RNA (ADAR1 and ADAR2) are human RNA-editing adenosine deaminases responsible for the conversion of adenosine to inosine at specific locations in cellular RNAs. Since inosine is recognized during translation as guanosine, this often results in the expression of protein sequences different from those encoded in the genome. While our knowledge of the ADAR2 structure and catalytic mechanism has grown over the years, our knowledge of ADAR1 has lagged. This is due, at least in part, to the lack of well defined, small RNA substrates useful for mechanistic studies of ADAR1. Here, we describe an ADAR1 substrate RNA that can be prepared by a combination of chemical synthesis and enzymatic ligation. Incorporation of adenosine analogs into this RNA and analysis of the rate of ADAR1 catalyzed deamination revealed similarities and differences in the way the ADARs recognize the edited nucleotide. Importantly, ADAR1 is more dependent than ADAR2 on the presence of N7 in the edited base. This difference between ADAR1 and ADAR2 appears to be dependent on the identity of a single amino acid residue near the active site. Thus, this work provides an important starting point in defining mechanistic differences between two functionally distinct human RNA editing ADARs.     

The E3 ubiquitin ligase adaptor Ndfip1 regulates Th17 differentiation by limiting the production of proinflammatory cytokines

Ndfip1 is an adaptor for the E3 ubiquitin ligase Itch. Both Ndfip1- and Itch-deficient T cells are biased toward Th2 cytokine production. In this study, we demonstrate that lungs from Ndfip1(-/-) mice showed increased numbers of neutrophils and Th17 cells. This was not because Ndfip1(-/-) T cells are biased toward Th17 differentiation. In fact, fewer Ndfip1(-/-) T cells differentiated into Th17 cells in vitro due to high IL-4 production. Rather, Th17 differentiation was increased in Ndfip1(-/-) mice due to increased numbers of IL-6-producing eosinophils. IL-6 levels in mice that lacked both Ndfip1 and IL-4 were similar to wild-type controls, and these mice had fewer Th17 cells in their lungs. These results indicate that Th2 inflammation, such as that observed in Ndfip1(-/-) mice, can increase Th17 differentiation by recruiting IL-6-producing eosinophils into secondary lymphoid organs and tissues. This may explain why Th17 cells develop within an ongoing Th2 inflammatory response.     

Asymptotic confidence intervals for the difference between two binomial parameters for use with small samples

Some asymptotically-based confidence intervals for the difference between the binomial parameters from two binomial populations are described. Five of these, including the usual simple interval, are extensively evaluated in terms of actual confidence level and interval length. A new simple interval behaves much better than the usual interval, as do some recently proposed iteratively computed intervals.     

The composition and flow of parotid saliva during acute hyperkalaemia in sodium-deficient sheep.

Sheep were infused intravenously with 0-43 M-KCl at 2 ml/min for 2 hr while they were either sodium-replete or sodium-deficient after the unilateral loss of parotid saliva for 18 hr or 3 days. Salivary flow was depressed during potassium infusion and the flow rates observed at maximum hyperkalaemia were similar in all three states of sodium balance despite the large differences in flow rate before potassium infusion. The fall in salivary Na/K ratio during potassium administration was diphasic, the initial decline being slow and followed by a more rapid fall in the ratio. The duration of the initial period of slow decline in this ratio ranged from 75-105 min, 45-60 min, and about 15 min in the sodium-replete, mildly sodium-deficient and severely sodium-deficient states respectively. The decline in salivary flow during sodium depletion was associated with decreasing salivary bicarbonate concentration and increasing salivary phosphate and hydrogen ion concentrations with the concentration of chloride showing no consistent trend. During acute hyperkalaemia the chloride and phosphate concentrations were negatively correlated with salivary flow, the bicarbonate concentration was positively correlated with flow and the hydrogen ion concentration was unaltered. The sodium concentration of the saliva showed a statistically significant correlation with flow only when the sheep were severely sodium-deficient.     

Minerals leached into drinking water from rubber stoppers.

Drinking water and its delivery system are potential sources of variation in animal research. Concern arose that rubber stoppers used to cork water bottles might be a source of some nutritionally required minerals which could leach into drinking water. Six types of stoppers, each having different compositions, were cleaned with stainless-steel sipper tubes inserted into them and attached to polypropylene bottles filled with either deionized water (pH 4.5) or acidified-deionized water (pH 2.5). After six days of contact, water levels of copper, magnesium, iron, manganese, zinc, chromium, and selenium were determined by atomic absorption spectroscopy. Additionally, three of the stopper types were analyzed for mineral content. Minerals were present in both stoppers and drinking water. Acidified-deionized water generally leached minerals from the stoppers than did deionized water. The black stopper which is commonly used in animal facilities contained and leached measurable levels of some minerals, but it still can be recommended for typical animal husbandry uses, although other types of stoppers would be more suitable for specific nutritional and toxicologic studies.