Hepatitis C virus NS5A is a direct substrate of casein kinase I-alpha, a cellular kinase identified by inhibitor affinity chromatography using specific NS5A hyperphosphorylation inhibitors

The hepatitis C virus encodes a single polyprotein that is processed by host and viral proteases to yield at least 10 mature viral proteins. The nonstructural (NS) protein 5A is a phosphoprotein, and experimental data indicate that the phosphorylation state of NS5A is important for the outcome of viral RNA replication. We were able to identify kinase inhibitors that specifically inhibit the formation of the hyperphosphorylated form of NS5A (p58) in cells. These kinase inhibitors were used for inhibitor affinity chromatography in order to identify the cellular targets of these compounds. The kinases casein kinase I (CKI), p38 MAPK, CIT (Citron Rho-interacting kinase), GAK, JNK2, PKA, RSK1/2, and RIPK2 were identified in the high affinity binding fractions of two NS5A hyperphosphorylation inhibitors (NS5A-p58-i). Even though these kinases are targets of the NS5A-p58-i, the only kinase showing an effect on NS5A hyperphosphorylation was confirmed to be CKI-alpha. Although this finding does not exclude the possibility that other kinase(s) might be involved in basal or regulatory phosphorylation of NS5A, we show here that NS5A is a direct substrate of CKI-alpha. Moreover, in vitro phosphorylation of NS5A by CKI-alpha resulted for the first time in the production of basal and hyperphosphorylated forms resembling those produced in cells. In vitro kinase reactions performed with NS5A peptides show that Ser-2204 is a preferred substrate residue for CKI-alpha after pre-phosphorylation of Ser-2201.     

Effect of the inclusion of food waste in pig diets on growth performance, carcass and meat quality

Food waste from fish and fruit shops was used as an alternative to the grain in grower-finisher pig diets. Two diets were formulated on an iso-nutrient basis (14 MJ digestible energy per kg, 160 g crude protein per kg on a dry-matter basis) to contain 0 g of food waste per kg in the control diet and 50 g of fish-shop waste per kg and 120 g of fruit-shop waste per kg in the experimental diet. In the study, 28 pigs per diet (seven pigs per pen) were fed ad libitum from 20 kg to 100 kg, then, they were slaughtered and the carcass characteristics determined. The inclusion of food waste in the diet had no significant effect (P>0.05) on average daily feed intake (2.12 v. 2.20 kg/day), average daily gain (0.74 v. 0.78 kg/day), or gain/feed (0.35 v. 0.35 kg per kg). In the case of the experimental diet, backfat thickness was significantly lower (18.0 v. 21.3 mm, P < 0.01). The results of the taste test indicated that the meat from food waste-fed pigs had acceptable organoleptic quality although a very light aroma to fish was observed in the bacon (P < 0.01).It was concluded that food waste from the fish and fruit shops could be included in grower-finisher pig diets without any detrimental effect on growth performance and only minor effects on carcass characteristics and meat quality.     

Diagnosing idiopathic learning disability: a cost-effectiveness analysis of microarray technology in the National Health Service of the United Kingdom

Array based comparative genomic hybridisation (aCGH) is a powerful technique for detecting clinically relevant genome imbalance and can offer 40 to > 1000 times the resolution of karyotyping. Indeed, idiopathic learning disability (ILD) studies suggest that a genome-wide aCGH approach makes 10–15% more diagnoses involving genome imbalance than karyotyping. Despite this, aCGH has yet to be implemented as a routine NHS service. One significant obstacle is the perception that the technology is prohibitively expensive for most standard NHS clinical cytogenetics laboratories. To address this, we investigated the cost-effectiveness of aCGH versus standard cytogenetic analysis for diagnosing idiopathic learning disability (ILD) in the NHS. Cost data from four participating genetics centres were collected and analysed. In a single test comparison, the average cost of aCGH was ￡442 and the average cost of karyotyping was ￡117 with array costs contributing most to the cost difference. This difference was not a key barrier when the context of follow up diagnostic tests was considered. Indeed, in a hypothetical cohort of 100 ILD children, aCGH was found to cost less per diagnosis (￡3,118) than a karyotyping and multi-telomere FISH approach (￡4,957). We conclude that testing for genomic imbalances in ILD using microarray technology is likely to be cost-effective because long-term savings can be made regardless of a positive (diagnosis) or negative result. Earlier diagnoses save costs of additional diagnostic tests. Negative results are cost-effective in minimising follow-up test choice. The use of aCGH in routine clinical practice warrants serious consideration by healthcare providers. Copyright statement The Corresponding Author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive licence (or non exclusive for government employees) on a worldwide basis to the BMJ Publishing Group Ltd, and its Licensees to permit this article (if accepted) to be published in BMJ editions and any other BMJPGL products and to exploit all subsidiary rights, as set out in our licence (bmj.com/advice/copyright.shtml). Authorship The authors included on this paper fulfil the criteria of authorship and no one who fulfils the criteria has been excluded from authorship. The authors made a substantial contribution to the conception, design, analysis and interpretation of data. They were involved in drafting the article or revising it critically for important intellectual content and approving the version to be published. Contributorship Sarah Wordsworth (Guarantor): Planning, conducting and reporting work, interpretation of data, drafting and revising article. James Buchanan: Conducting and reporting work, interpretation of data, revising article. Regina Regan: Completing costing questionnaire, providing protocol details, other costing information, interpretation of data, information about learning disability and genome imbalance and revising article. Val Davison: Completing costing questionnaire, providing protocol details, sharing overall laboratory experience and drafting article. Kim Smith: Completing costing questionnaire, providing protocol details, drafting article. Sara Dyer: Completing costing questionnaire and providing protocol details. Carolyn Campbell: Completing costing questionnaire and providing protocol details. Edward Blair: Critical appraisal of article for clinical content and revising article. Eddy Maher: Completing costing questionnaire, providing protocol details, sharing overall laboratory experience and drafting article. Jenny Taylor: Planning and facilitating work between centres. Drafting and revising article. Samantha JL Knight: Completing costing questionnaire, providing protocol details, other costing information, interpretation of data, providing information about learning disability and genome imbalance, drafting and revising article. Jenny Taylor and Samantha JL Knight contributed equally to the work presented.     

Habitat fragmentation, variable edge effects, and the landscape-divergence hypothesis

Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world's largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: forest dynamics varied somewhat with fragment age, but also fluctuated markedly over time, evidently because of sporadic droughts and windstorms. Given the acute sensitivity of habitat fragments to local landscape and weather dynamics, we predict that fragments within the same landscape will tend to converge in species composition, whereas those in different landscapes will diverge in composition. This 'landscape-divergence hypothesis', if generally valid, will have key implications for biodiversity-conservation strategies and for understanding the dynamics of fragmented ecosystems.     

Short-term effects of a "health-at-every-size" approach on eating behaviors and appetite ratings

Objective: To assess the effects of a “Health‐At‐Every‐Size” (HAES) intervention on eating behaviors and appetite ratings in 144 premenopausal overweight women. Research Methods and Procedures: Women were randomly assigned to one of the 3 groups: HAES group, social support (SS) group, and control group (N = 48 in each group). Interventions were conducted over a 4‐month period, and measurements were taken before and after this period. Eating behaviors (cognitive dietary restraint, disinhibition, and susceptibility to hunger) were evaluated by the Three‐Factor Eating Questionnaire. Appetite ratings (desire to eat, hunger, fullness, and prospective food consumption) were assessed by visual analogue scales before and after a standardized breakfast. Results: More important decreases in susceptibility to hunger and external hunger were observed in the HAES group when compared with the SS group (p = 0.05, for susceptibility to hunger) and the control group (p = 0.02 and p = 0.005, for susceptibility to hunger and external hunger, respectively). In addition, women from the HAES group had more important decreases in postprandial area under the curve for desire to eat (p = 0.02) and hunger (p = 0.04) when compared with the control group. The change in the desire to eat noted in the HAES group was also different from the one observed in SS group (p = 0.02). Women from the HAES group experienced significant weight loss at 4 months (?1.6 ± 2.5 kg, p < 0.0001), which did not differ significantly from the SS and control groups (p = 0.09). An increase in flexible restraint was significantly related to a greater weight loss in both HAES and SS groups (r = ?0.39, p < 0.01; and r = ?0.37, p < 0.05, respectively). A decrease in habitual susceptibility to disinhibition was also associated with a greater weight loss in HAES and control groups (r = 0.31, p < 0.05; and r = 0.44, p < 0.05, respectively). Discussion: These results suggest that a HAES intervention could have significant effects on eating behaviors and appetite ratings in premenopausal overweight women, when compared with an SS intervention or a control group.     

B chromosomes in popcorn (Zea mays L.)

Cytological analysis of microsporogenesis in 72 popcorn plants, comprising nine from the original population (CMS-43, S(0)) and 63 from seven cycles of self-fertilization (S(1) to S(7)), one plant of S(0) generation (plant 2) was identified with B chromosomes. The number of B chromosomes varied from two to three in the same anther. The pattern of chromosome pairing and meiotic behavior of Bs were similar to those found in other plant species. The presence of B chromosomes did not affect chiasma frequency and chiasma distribution in A chromosomes. This is the first report of B chromosomes in popcorn.     

Finding protein-protein interaction patterns by contact map matching

We propose a novel method for defining patterns of contacts present in protein-protein complexes. A new use of the traditional contact maps (more frequently used for representation of the intra-chain contacts) is presented for analysis of inter-chain contacts. Using an algorithm based on image processing techniques, we can compare protein-protein interaction maps and also obtain a dissimilarity score between them. The same algorithm used to compare the maps can align the contacts of all the complexes and be helpful in the determination of a pattern of conserved interactions at the interfaces. We present an example for the application of this method by analyzing the pattern of interaction of bovine pancreatic trypsin inhibitors and trypsins, chymotrypsins, a thrombin, a matriptase, and a kallikrein - all classified as serine proteases. We found 20 contacts conserved in trypsins and chymotrypsins and 3 specific ones are present in all the serine protease complexes studied. The method was able to identify important contacts for the protein family studied and the results are in agreement with the literature.