Progress with the PRINTS protein fingerprint database.

PRINTS is a compendium of protein motif 'fingerprints' derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. To date, 400 fingerprints have been constructed and stored in Prints, the size of which has doubled in the last year. The current version, 9.0, encodes approximately 2000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbours. PRINTS thus provides a useful adjunct to the widely used PROSITE dictionary of patterns. The database is now accessible via the Database Browser on the UCL Bioinformatics server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser .     

Surveying Rubisco Diversity and Temperature Response to Improve Crop Photosynthetic Efficiency

The threat to global food security of stagnating yields and population growth makes increasing crop productivity a critical goal over the coming decades. One key target for improving crop productivity and yields is increasing the efficiency of photosynthesis. Central to photosynthesis is Rubisco, which is a critical but often rate-limiting component. Here, we present full Rubisco catalytic properties measured at three temperatures for 75 plants species representing both crops and undomesticated plants from diverse climates. Some newly characterized Rubiscos were naturally “better” compared to crop enzymes and have the potential to improve crop photosynthetic efficiency. The temperature response of the various catalytic parameters was largely consistent across the diverse range of species, though absolute values showed significant variation in Rubisco catalysis, even between closely related species. An analysis of residue differences among the species characterized identified a number of candidate amino acid substitutions that will aid in advancing engineering of improved Rubisco in crop systems. This study provides new insights on the range of Rubisco catalysis and temperature response present in nature, and provides new information to include in models from leaf to canopy and ecosystem scale.In a changing climate and under pressure from a population set to hit nine billion by 2050, global food security will require massive changes to the way food is produced, distributed, and consumed (Ort et al., 2015). To match rising demand, agricultural production must increase by 50 to 70% in the next 35 years, and yet the gains in crop yields initiated by the green revolution are slowing, and in some cases, stagnating (Long and Ort, 2010; Ray et al., 2012). Among a number of areas being pursued to increase crop productivity and food production, improving photosynthetic efficiency is a clear target, offering great promise (Parry et al., 2007; von Caemmerer et al., 2012; Price et al., 2013; Ort et al., 2015). As the gatekeeper of carbon entry into the biosphere and often acting as the rate-limiting step of photosynthesis, Rubisco, the most abundant enzyme on the planet (Ellis, 1979), is an obvious and important target for improving crop photosynthetic efficiency.Rubisco is considered to exhibit comparatively poor catalysis, in terms of catalytic rate, specificity, and CO₂ affinity (Tcherkez et al., 2006; Andersson, 2008), leading to the suggestion that even small increases in catalytic efficiency may result in substantial improvements to carbon assimilation across a growing season (Zhu et al., 2004; Parry et al., 2013; Galmés et al., 2014a; Carmo-Silva et al., 2015). If combined with complimentary changes such as optimizing other components of the Calvin Benson or photorespiratory cycles (Raines, 2011; Peterhansel et al., 2013; Simkin et al., 2015), optimized canopy architecture (Drewry et al., 2014), or introducing elements of a carbon concentrating mechanism (Furbank et al., 2009; Lin et al., 2014a; Hanson et al., 2016; Long et al., 2016), Rubisco improvement presents an opportunity to dramatically increase the photosynthetic efficiency of crop plants (McGrath and Long, 2014; Long et al., 2015; Betti et al., 2016). A combination of the available strategies is essential for devising tailored solutions to meet the varied requirements of different crops and the diverse conditions under which they are typically grown around the world.Efforts to engineer an improved Rubisco have not yet produced a “super Rubisco” (Parry et al., 2007; Ort et al., 2015). However, advances in engineering precise changes in model systems continue to provide important developments that are increasing our understanding of Rubisco catalysis (Spreitzer et al., 2005; Whitney et al., 2011a, 2011b; Morita et al., 2014; Wilson et al., 2016), regulation (Andralojc et al., 2012; Carmo-Silva and Salvucci, 2013; Bracher et al., 2015), and biogenesis (Saschenbrecker et al., 2007; Whitney and Sharwood, 2008; Lin et al., 2014b; Hauser et al., 2015; Whitney et al., 2015).A complementary approach is to understand and exploit Rubisco natural diversity. Previous characterization of Rubisco from a limited number of species has not only demonstrated significant differences in the underlying catalytic parameters, but also suggests that further undiscovered diversity exists in nature and that the properties of some of these enzymes could be beneficial if present in crop plants (Carmo-Silva et al., 2015). Recent studies clearly illustrate the variation possible among even closely related species (Galmés et al., 2005, 2014b, 2014c; Kubien et al., 2008; Andralojc et al., 2014; Prins et al., 2016).Until recently, there have been relatively few attempts to characterize the consistency, or lack thereof, of temperature effects on in vitro Rubisco catalysis (Sharwood and Whitney, 2014), and often studies only consider a subset of Rubisco catalytic properties. This type of characterization is particularly important for future engineering efforts, enabling specific temperature effects to be factored into any attempts to modify crops for a future climate. In addition, the ability to coanalyze catalytic properties and DNA or amino acid sequence provides the opportunity to correlate sequence and biochemistry to inform engineering studies (Christin et al., 2008; Kapralov et al., 2011; Rosnow et al., 2015). While the amount of gene sequence information available grows rapidly with improving technology, knowledge of the corresponding biochemical variation resulting has yet to be determined (Cousins et al., 2010; Carmo-Silva et al., 2015; Sharwood and Whitney, 2014; Nunes-Nesi et al., 2016).This study aimed to characterize the catalytic properties of Rubisco from diverse species, comprising a broad range of monocots and dicots from diverse environments. The temperature dependence of Rubisco catalysis was evaluated to tailor Rubisco engineering for crop improvement in specific environments. Catalytic diversity was analyzed alongside the sequence of the Rubisco large subunit gene, rbcL, to identify potential catalytic switches for improving photosynthesis and productivity. In vitro results were compared to the average temperature of the warmest quarter in the regions where each species grows to investigate the role of temperature in modulating Rubisco catalysis.     

Host tissue identification for cryptic hymenopteran parasitoids associated with Sirex noctilio

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Human amylin proteotoxicity impairs protein biosynthesis,and alters major cellular signaling pathways in the heart,brain and liver of humanized diabetic rat model in vivo

Introduction

Chronic hypersecretion of the 37 amino acid amylin is common in type 2 diabetics (T2D). Recent studies implicate human amylin aggregates cause proteotoxicity (cell death induced by misfolded proteins) in both the brain and the heart.

Objectives

Identify systemic mechanisms/markers by which human amylin associated with cardiac and brain defects might be identified.

Methods

We investigated the metabolic consequences of amyloidogenic and cytotoxic amylin oligomers in heart, brain, liver, and plasma using non-targeted metabolomics analysis in a rat model expressing pancreatic human amylin (HIP model).

Results

Four metabolites were significantly different in three or more of the four compartments (heart, brain, liver, and plasma) in HIP rats. When compared to a T2D rat model, HIP hearts uniquely had significant DECREASES in five amino acids (lysine, alanine, tyrosine, phenylalanine, serine), with phenylalanine decreased across all four tissues investigated, including plasma. In contrast, significantly INCREASED circulating phenylalanine is reported in diabetics in multiple recent studies.

Conclusion

DECREASED phenylalanine may serve as a unique marker of cardiac and brain dysfunction due to hyperamylinemia that can be differentiated from alterations in T2D in the plasma. While the deficiency in phenylalanine was seen across tissues including plasma and could be monitored, reduced tyrosine was seen only in the brain. The 50 % reduction in phenylalanine and tyrosine in HIP brains is significant given their role in supporting brain chemistry as a precursor for catecholamines (dopamine, norepinephrine, epinephrine), which may contribute to the increased morbidity and mortality in diabetics at a multi-system level beyond the effects on glucose metabolism.

     

ELECTRON MICROSCOPE AUTORADIOGRAPHY OF ERYTHROID CELLS USING RADIOACTIVE IRON

The "circle analysis" method of Williams (1969) and a new improved method employing hypothetical grains described in the previous paper have been used to analyze the distribution of autoradiographic grains over erythroid bone marrow cells labeled with radioactive iron, ⁵⁵Fe. The resolution obtainable with this isotope was determined by measuring the distribution of grains about a thin line source. This distribution was also used in calculation of the circle size for the Williams's analysis and the distances of hypothetical grains for the new method. The new method provides estimates for the amount of activity in the regions of condensed and extended nuclear chromatin and for the concentration of isotope at the junction between these two areas. The possible significance of activity in this junctional region is discussed.     

Interaction between individuals during the colonisation of Douglas fir needles by sistentes of Adelges cooleyi

Summary A laboratory study of Adelges cooleyi sistentes emerging from diapause shows that the sistentes redistribute themselves over the needles in the form of aggregations. At low densities needle bases are preferred to the tips, this preference becoming less marked as sistentes density increases. Within each needle aggregation a certain amount of spacing out occurs which minimises the number of sistentes settling in close proximity. Over a given period of time adult sistentes produce more eggs at the base of the needles than at the tips. The settling behaviour ensures that at low densities the most favourable parts of the needle at the base are utilised first while the spacing out factor provides sufficient space for the development of the egg masses and minimises the possibility of over-exploitation of one part of the needle in relation to the remainder.     

Genetic linkage of von Recklinghausen neurofibromatosis to the nerve growth factor receptor gene

von Recklinghausen neurofibromatosis (VRNF) is one of the most common inherited disorders affecting the human nervous system. VRNF is transmitted as an autosomal dominant defect with high penetrance but variable expressivity. The disorder is characterized clinically by hyperpigmented patches of skin (café au lait macules, axillary freckles) and by multiple tumors of peripheral nerve, spinal nerve roots, and brain (neurofibromas, optic gliomas). These tumors can cause disfigurement, paralysis, blindness, and death. We have determined the chromosomal location of the VRNF gene by genetic linkage analysis using DNA markers. The VRNF gene is genetically linked to the locus encoding nerve growth factor receptor, located on the long arm of chromosome 17 in the region 17q12----17q22. However, crossovers with the VRNF locus suggest that a mutation in the nerve growth factor receptor gene itself is unlikely to be the fundamental defect responsible for the VRNF phenotype.     

Reconstruction of the burned nipple-areola complex

Reconstructive results of 115 burned nipple-areola complexes in 84 female patients were reviewed. Results of nipple reconstruction using local quadrapod flaps (33 percent good, 45 percent fair, 22 percent poor) and composition grafts from the earlobe (20 percent good, 60 percent fair, 20 percent poor) were comparable, and both were superior to results obtained with the "double-bubble" technique (24 percent good, 35 percent fair, 41 percent poor). Differences in nipple reconstruction techniques were not appreciated until 1 year postoperatively. The early appearance of areola reconstruction with tattooing and split-thickness grafts was excellent. However, significant late hypopigmentation changes were observed with both techniques. Areola reconstruction with full-thickness skin grafts from the superomedial thigh (47 percent good, 33 percent fair, 20 percent poor) were superior to those obtained with tattooing (14 percent good, 35 percent fair, 51 percent poor) and split-thickness skin grafts from the contralateral unburned areola (21 percent good, 21 percent fair, 58 percent poor). We recommend employing local quadrapod flaps (for nipple), provided there is adequate surrounding dermis, and full-thickness skin grafts (for areola) in the reconstruction of the burned breast.