NMR analysis of synthetic human serum albumin alpha-helix 28 identifies structural distortion upon amadori modification

The non-enzymatic reaction between reducing sugars and long-lived proteins in vivo results in the formation of glycation and advanced glycation end products, which alter the properties of proteins including charge, helicity, and their tendency to aggregate. Such protein modifications are linked with various pathologies associated with the general aging process such as Alzheimer disease and the long-term complications of diabetes. Although it has been suggested that glycation and advanced glycation end products altered protein structure and helicity, little structural data and information currently exist on whether or not glycation does indeed influence or change local protein secondary structure. We have addressed this problem using a model helical peptide system containing a di-lysine motif derived from human serum albumin. We have shown that, in the presence of 50 mM glucose and at 37 degrees C, one of the lysine residues in the di-lysine motif within this peptide is preferentially glycated. Using NMR analysis, we have confirmed that the synthetic peptide constituting this helix does indeed form a alpha-helix in solution in the presence of 30% trifluoroethanol. Glycation of the model peptide resulted in the distortion of the alpha-helix, forcing the region of the helix around the site of glycation to adopt a 3(10) helical structure. This is the first reported evidence that glycation can influence or change local protein secondary structure. The implications and biological significance of such structural changes on protein function are discussed

CydDC-mediated reductant export in Escherichia coli controls the transcriptional wiring of energy metabolism and combats nitrosative stress

The glutathione/cysteine exporter CydDC maintains redox balance in Escherichia coli. A cydD mutant strain was used to probe the influence of CydDC upon reduced thiol export, gene expression, metabolic perturbations, intracellular pH homeostasis, and tolerance to nitric oxide (NO). Loss of CydDC was found to decrease extracytoplasmic thiol levels, whereas overexpression diminished the cytoplasmic thiol content. Transcriptomic analysis revealed a dramatic up-regulation of protein chaperones, protein degradation (via phenylpropionate/phenylacetate catabolism), ?-oxidation of fatty acids, and genes involved in nitrate/nitrite reduction. 1H NMR metabolomics revealed elevated methionine and betaine and diminished acetate and NAD+ in cydD cells, which was consistent with the transcriptomics-based metabolic model. The growth rate and ?pH, however, were unaffected, although the cydD strain did exhibit sensitivity to the NO-releasing compound NOC-12. These observations are consistent with the hypothesis that the loss of CydDC-mediated reductant export promotes protein misfolding, adaptations to energy metabolism, and sensitivity to NO. The addition of both glutathione and cysteine to the medium was found to complement the loss of bd -type cytochrome synthesis in a cydD strain (a key component of the pleiotropic cydDC phenotype), providing the first direct evidence that CydDC substrates are able to restore the correct assembly of this respiratory oxidase. These data provide an insight into the metabolic flexibility of E. coli , highlight the importance of bacterial redox homeostasis during nitrosative stress, and report for the first time the ability of periplasmic low molecular weight thiols to restore haem incorporation into a cytochrome complex

Entrapment: an important mechanism to explain the shortwave 3D radiative effect of clouds

Several mechanisms have previously been proposed to explain differences between the shortwave reflectance of realistic cloud scenes computed using the 1D independent column approximation (ICA) and 3D solutions of the radiative transfer equation. When the sun is low in the sky, interception of sunlight by cloud sides tends to increase reflectance relative to ICA estimates that neglect this effect. When the sun is high, 3D radiative transfer tends to make clouds less reflective, which we argue is explained by the mechanism of “entrapment” whereby horizontal transport of radiation beneath a cloud layer increases the chances, relative to the ICA, of light being absorbed by cloud or the surface. It is especially important for multilayered cloud scenes. We describe modifications to the previously described Speedy Algorithm for Radiative Transfer through Cloud Sides (SPARTACUS) to represent different entrapment assumptions, and test their impact on 65 contrasting scenes from a cloud-resolving model. When entrapment is represented explicitly via a calculation of the mean horizontal distance traveled by reflected light, SPARTACUS predicts a mean “3D radiative effect” (the difference in top-of-atmosphere irradiances between 3D and ICA calculations) of 8.1 W m−2 for overhead sun. This is within 2% of broadband Monte Carlo calculations on the same scenes. The importance of entrapment is highlighted by the finding that the extreme assumptions in SPARTACUS of “zero entrapment” and “maximum entrapment” lead to corresponding mean 3D radiative effects of 1.7 and 19.6 W m−2, respectively

Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12)

It has been known for the past 20 years that two pathways exist in nature for the de novo biosynthesis of the coenzyme form of vitamin B12, adenosylcobalamin, representing aerobic and anaerobic routes. In contrast to the aerobic pathway, the anaerobic route has remained enigmatic because many of its intermediates have proven technically challenging to isolate, because of their inherent instability. However, by studying the anaerobic cobalamin biosynthetic pathway in Bacillus megaterium and using homologously overproduced enzymes, it has been possible to isolate all of the intermediates between uroporphyrinogen III and cobyrinic acid. Consequently, it has been possible to detail the activities of purified cobinamide biosynthesis (Cbi) proteins CbiF, CbiG, CbiD, CbiJ, CbiET, and CbiC, as well as show the direct in vitro conversion of 5-aminolevulinic acid into cobyrinic acid using a mixture of 14 purified enzymes. This approach has resulted in the isolation of the long sought intermediates, cobalt-precorrin-6A and -6B and cobalt-precorrin-8. EPR, in particular, has proven an effective technique in following these transformations with the cobalt(II) paramagnetic electron in the dyz orbital, rather than the typical dz2. This result has allowed us to speculate that the metal ion plays an unexpected role in assisting the interconversion of pathway intermediates. By determining a function for all of the pathway enzymes, we complete the tool set for cobalamin biosynthesis and pave the way for not only enhancing cobalamin production, but also design of cobalamin derivatives through their combinatorial use and modification

Montreal Protocol

DATE: Signed September 16, 1987; took effect January 1, 1989; amended 1990, 1992, 1995, 1997, and 1999 The Montreal Protocol was created to help preserve the Earth’s ozone layer by severely limiting the production and use of chlorofluorocarbons (CFCs ) and other halogenated compounds

Pancreatic Cancer Signature Center: Providing the Research Tools Necessary to Advance Pancreatic Cancer Patient Care

poster abstractThere were approximately 43,000 new cases of pancreatic ductal adenocarcinoma (PDAC) in the U.S. in 2010, and approximately 37,000 deaths. PDAC thus constitutes the fourth leading cause of cancer deaths, and PDAC patients have a dismal 5-year survival rate of 6%. PDAC is notoriously resistant to chemotherapy and radiation and even with our best treatment options, a complete margin-negative surgical resection, few patients achieving long-term survival. Despite these statistics, surprisingly only a small number of NCI-designated cancer centers have a specialized pancreatic cancer program. The creation of the IUPUI Signature Center for Pancreatic Cancer Research has been the foundation for putting IUPUI, the IU School of Medicine, Purdue University and the IU Simon Cancer Center at the forefront of pancreatic cancer treatment and research across the nation. The Signature Center, comprised of basic, translational and clinical researchers, represents the continuum of the disease from biological / molecular investigation to clinical trials. Funding from the Signature Center Initiative is being utilized to develop genetically engineered mouse models, orthotopic pancreatic cancer models as well as a human pancreatic cancer xenograft model. Establishment and characterization of these in vivo models provides the groundwork to be used by all members in their translational research projects. Additionally, work has begun on a web portal to promote and educate both patients and clinicians about the IUSCC Pancreas Cancer Clinic which became operational in 2010. Taken together the development of these in vivo models as well as web support of the Pancreas Cancer Clinic provides the infrastructure to support pancreas cancer research across the continuum of bench to bedside to practice. The availability of these resources to all members promotes inter-disciplinary collaborations aimed at increasing our understanding of pancreatic cancer so that advancements can be made in diagnosis, prevention and treatment of this malignancy

Do neighbourhood environmental perceptions affect practices?

In this paper, we examine how environmental practices related to public transit and urban green space use are influenced by perceptions of local level environmental change, neighbourhood inhabitation, and socio-demographic factors. The analysis shows that perceptions of change and neighbourhood inhabitation offer better explanations for changing local environmental practices than socio-demographic orientations. We contribute to social practice theory by drawing attention to the interplay of environmental perceptions and neighbourhood inhabitation as factors that facilitate changing environmental practices. By gaining insight into the relationship between perceptions of change and environmental practices, we thereby learn how sustainability goals, such as those embodied by SDG11, can be translated into social practices at the community level.Dans cet article, nous examinons comment les pratiques environnementales liées au transport en commun et à l’utilisation des espaces verts urbains sont influencées par les perceptions du changement environnemental au niveau local, l’habitation des quartiers et les facteurs sociodémographiques. L’analyse montre que les perceptions du changement et de l’habitat du quartier offrent de meilleures explications pour l’évolution des pratiques environnementales locales que les orientations sociodémographiques. Nous contribuons è la théorie de la pratique sociale en attirant l’attention sur l’interaction des perceptions environnementales et de l’habitation du quartier en tant que facteurs qui facilitent l’évolution des pratiques environnementales. En acquérant un aperçu de la relation entre les perceptions du changement et les pratiques environnementales, nous apprenons ainsi comment les objectifs de durabilité, tels que ceux incarnées par ODD (Agenda 2030 du développement durable), peuvent être traduits en pratiques sociales au niveau communautaire

Entanglement of indistinguishable particles in condensed matter physics

The concept of entanglement in systems where the particles are indistinguishable has been the subject of much recent interest and controversy. In this paper we study the notion of entanglement of particles introduced by Wiseman and Vaccaro [Phys. Rev. Lett. 91, 097902 (2003)] in several specific physical systems, including some that occur in condensed matter physics. The entanglement of particles is relevant when the identical particles are itinerant and so not distinguished by their position as in spin models. We show that entanglement of particles can behave differently to other approaches that have been used previously, such as entanglement of modes (occupation-number entanglement) and the entanglement in the two-spin reduced density matrix. We argue that the entanglement of particles is what could actually be measured in most experimental scenarios and thus its physical significance is clear. This suggests entanglement of particles may be useful in connecting theoretical and experimental studies of entanglement in condensed matter systems.Comment: 13 pages, 6 figures, comments welcome, published version (minor changes, added references