Cofactor mobility determines reaction outcome in the IMPDH and GMPR (β-α)8 barrel enzymes

Inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate reductase (GMPR) belong to the same structural family, share a common set of catalytic residues and bind the same ligands. The structural and mechanistic features that determine reaction outcome in the IMPDH and GMPR family have not been identified. Here we show that the GMPR reaction uses the same intermediate E-XMP* as IMPDH, but in this reaction the intermediate reacts with ammonia instead of water. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimics a distinct step in the catalytic cycle of GMPR. The cofactor is found in two conformations: an 'in' conformation poised for hydride transfer and an 'out' conformation in which the cofactor is 6 ? from IMP. Mutagenesis along with substrate and cofactor analog experiments demonstrate that the out conformation is required for the deamination of GMP. Remarkably, the cofactor is part of the catalytic machinery that activates ammonia.     

Mutations in or near the transmembrane domain alter PMEL amyloid formation from functional to pathogenic

PMEL is a pigment cell-specific protein that forms physiological amyloid fibrils upon which melanins ultimately deposit in the lumen of the pigment organelle, the melanosome. Whereas hypomorphic PMEL mutations in several species result in a mild pigment dilution that is inherited in a recessive manner, PMEL alleles found in the Dominant white (DW) chicken and Silver horse (HoSi)--which bear mutations that alter the PMEL transmembrane domain (TMD) and that are thus outside the amyloid core--are associated with a striking loss of pigmentation that is inherited in a dominant fashion. Here we show that the DW and HoSi mutations alter PMEL TMD oligomerization and/or association with membranes, with consequent formation of aberrantly packed fibrils. The aberrant fibrils are associated with a loss of pigmentation in cultured melanocytes, suggesting that they inhibit melanin production and/or melanosome integrity. A secondary mutation in the Smoky chicken, which reverts the dominant DW phenotype, prevents the accumulation of PMEL in fibrillogenic compartments and thus averts DW-associated pigment loss; a secondary mutation found in the Dun chicken likely dampens a HoSi-like dominant mutation in a similar manner. We propose that the DW and HoSi mutations alter the normally benign amyloid to a pathogenic form that antagonizes melanosome function, and that the secondary mutations found in the Smoky and Dun chickens revert or dampen pathogenicity by functioning as null alleles, thus preventing the formation of aberrant fibrils. We speculate that PMEL mutations can model the conversion between physiological and pathological amyloid.     

Resource and Climate Implications of Landfill Mining

This study analyzes the amount of material deposited in Swedish municipal solid waste landfills, how much is extractable and recyclable, and what the resource and climate implications are if landfill mining coupled with resource recovery were to be implemented in Sweden. The analysis is based on two scenarios with different conventional separation technologies, one scenario using a mobile separation plant and the other using a more advanced stationary separation plant. Further, the approach uses Monte Carlo simulation to address the uncertainties attached to each of the different processes in the scenarios. Results show that Sweden's several thousand municipal landfills contain more than 350 million tonnes (t) of material. If landfill mining combined with resource recovery is implemented using a contemporary stationary separation plant, it would be possible to extract about 7 million t of ferrous metals and 2 million t of nonferrous metals, enough to meet the demand of Swedish industry for ferrous and nonferrous metals for three and eight years, respectively. This study further shows that landfill mining could potentially lead to the equivalent of a one‐time reduction of about 50 million t of greenhouse gas emissions (carbon‐dioxide equivalents), corresponding to 75% of Sweden's annual emissions.     

Genotyping by RAD sequencing enables mapping of fatty acid composition traits in perennial ryegrass (Lolium perenne (L.))

Perennial ryegrass (Lolium perenne L.) is the most important forage crop in temperate livestock agriculture. Its nutritional quality has significant impact on the quality of meat and milk for human consumption. Evidence suggests that higher energy content in forage can assist in reducing greenhouse gas emissions from ruminants. Increasing the fatty acid content (especially α‐linolenic acid, an omega‐3 fatty acid) may thus contribute to better forage, but little is known about the genetic basis of variation for this trait. To this end, quantitative trait loci (QTLs) were identified associated with major fatty acid content in perennial ryegrass using a population derived from a cross between the heterozygous and outbreeding high‐sugar grass variety AberMagic and an older variety, Aurora. A genetic map with 434 restriction‐associated DNA (RAD) and SSR markers was generated. Significant QTLs for the content of palmitic (C16:0) on linkage groups (LGs) 2 and 7; stearic (C18:0) on LGs 3, 4 and 7; linoleic (C18:2n‐6) on LGs 2 and 5; and α‐linolenic acids (C18:3n‐3) on LG 1 were identified. Two candidate genes (a lipase and a beta‐ketoacyl CoA synthase), both associated with C16:0, and separately with C18:2n‐6 and C18:0 contents, were identified. The physical positions of these genes in rice and their genetic positions in perennial ryegrass were consistent with established syntenic relationships between these two species. Validation of these associations is required, but the utility of RAD markers for rapid generation of genetic maps and QTL analysis has been demonstrated for fatty acid composition in a global forage crop.     

Normalized difference vegetation index (NDVI) as a predictor of forage availability for ungulates in forest and field habitats

Quantifying available plant biomass is a crucial step towards improving our understanding of herbivore ecology and trophic interactions. Thanks to the development of satellite-derived vegetation indices such as the normalized difference vegetation index (NDVI), ecologists have been provided with indirect estimates of primary production at various temporal and spatial scales. When it comes to forested ecosystems, most mammalian herbivores predominantly rely on the ground vegetation, yet little is known regarding the suitability of NDVI to predict this component of forest vegetation cover. This study compares the relationship between NDVI and ground vegetation biomass in two contrasting habitats (field and forest) in Eastern Poland over the spring and summer seasons (2007–2008). Results indicate that seasonality shapes the relationship between NDVI and ground vegetation biomass for each habitat type. In the field habitat, NDVI and ground vegetation biomass were positively related, with a stronger correlation between the two variables occurring in summer. In the forest habitat, a switch in the direction of the correlation between biomass and NDVI (from positive in spring to negative in summer) was detected. The timing of the switch was related to the timing of full development of tree and shrub leaves (late May–early June). This suggests that the usefulness of NDVI as a predictor of ground vegetation biomass is dependent upon the habitat considered and the targeted season.     

The DIAMOND initiative: implementing collaborative care for depression in 75 primary care clinics

Background

The many randomized trials of the collaborative care model for improving depression in primary care have not described the implementation and maintenance of this model. This paper reports how and the degree to which collaborative care process changes were implemented and maintained for the 75 primary care clinics participating in the DIAMOND Initiative (Depression Improvement Across Minnesota–Offering a New Direction).

Methods

Each clinic was trained to implement seven components of the model and participated in ongoing evaluation and facilitation activities. For this study, assessment of clinical process implementation was accomplished via completion of surveys by the physician leader and clinic manager of each clinic site at three points in time. The physician leader of each clinic completed a survey measure of the presence of various practice systems prior to and one and two years after implementation. Clinic managers also completed a survey of organizational readiness and the strategies used for implementation.

Results

Survey response rates were 96% to 100%. The systems survey confirmed a very high degree of implementation (with large variation) of DIAMOND depression practice systems (mean of 24.4?±?14.6%) present at baseline, 57.0?±?21.0% at one year (P?=?<0.0001), and 55.9?±?21.3% at two years. There was a similarly large increase (and variation) in the use of various quality improvement strategies for depression (mean of 29.6?±?28.1% at baseline, 75.1?±?22.3% at one year (P?=?<0.0001), and 74.6?±?23.0% at two years.

Conclusions

This study demonstrates that under the right circumstances, primary care clinics that are prepared to implement evidence-based care can do so if financial barriers are reduced, effective training and facilitation are provided, and the new design introduces the specific mental models, new care processes, and workers and expertise that are needed. Implementation was associated with a marked increase in the number of improvement strategies used, but actual care and outcomes data are needed to associate these changes with patient outcomes and patient-reported care.

     

Polymorphism in the Retinoic Acid Metabolizing Enzyme CYP26B1 and the Development of Crohn’s Disease

Several studies suggest that Vitamin A may be involved in the pathogenesis of inflammatory bowel disease (IBD), but the mechanism is still unknown. Cytochrome P450 26 B1 (CYP26B1) is involved in the degradation of retinoic acid and the polymorphism rs2241057 has an elevated catabolic function of retinoic acid, why we hypothesized that the rs2241057 polymorphism may affect the risk of Crohn’s disease (CD) and Ulcerative Colitis (UC). DNA from 1378 IBD patients, divided into 871 patients with CD and 507 with UC, and 1205 healthy controls collected at Örebro University Hospital and Karolinska University Hospital were analyzed for the CYP26B1 rs2241057 polymorphism with TaqMan® SNP Genotyping Assay followed by allelic discrimination analysis. A higher frequency of patients homozygous for the major (T) allele was associated with CD but not UC compared to the frequency found in healthy controls. A significant association between the major allele and non-stricturing, non-penetrating phenotype was evident for CD. However, the observed associations reached borderline significance only, after correcting for multiple testing. We suggest that homozygous carriers of the major (T) allele, relative to homozygous carriers of the minor (C) allele, of the CYP26B1 polymorphism rs2241057 may have an increased risk for the development of CD, which possibly may be due to elevated levels of retinoic acid. Our data may support the role of Vitamin A in the pathophysiology of CD, but the exact mechanisms remain to be elucidated.     

Gender Affects Skin Wound Healing in Plasminogen Deficient Mice

The fibrinolytic activity of plasmin plays a fundamental role in resolution of blood clots and clearance of extravascular deposited fibrin in damaged tissues. These vital functions of plasmin are exploited by malignant cells to accelerate tumor growth and facilitate metastases. Mice lacking functional plasmin thus display decreased tumor growth in a variety of cancer models. Interestingly, this role of plasmin has, in regard to skin cancer, been shown to be restricted to male mice. It remains to be clarified whether gender also affects other phenotypic characteristics of plasmin deficiency or if this gender effect is restricted to skin cancer. To investigate this, we tested the effect of gender on plasmin dependent immune cell migration, accumulation of hepatic fibrin depositions, skin composition, and skin wound healing. Gender did not affect immune cell migration or hepatic fibrin accumulation in neither wildtype nor plasmin deficient mice, and the existing differences in skin composition between males and females were unaffected by plasmin deficiency. In contrast, gender had a marked effect on the ability of plasmin deficient mice to heal skin wounds, which was seen as an accelerated wound closure in female versus male plasmin deficient mice. Further studies showed that this gender effect could not be reversed by ovariectomy, suggesting that female sex-hormones did not mediate the accelerated skin wound healing in plasmin deficient female mice. Histological examination of healed wounds revealed larger amounts of fibrotic scars in the provisional matrix of plasmin deficient male mice compared to female mice. These fibrotic scars correlated to an obstruction of cell infiltration of the granulation tissue, which is a prerequisite for wound healing. In conclusion, the presented data show that the gender dependent effect of plasmin deficiency is tissue specific and may be secondary to already established differences between genders, such as skin thickness and composition.