Investigating The Structural And Physiochemical Properties Of Collagen Mimetic Peptides With Modified Backbones

Collagen is the most abundant protein found in mammalian systems and is critically important in a myriad of different regulatory pathways, prompting widespread effort to model and understand collagen-protein interactions. A network of hydrogen bonds, non-covalent interactions, sterics, and stereoelectronic effects hold collagen’s unique triple-helical quaternary structure together. The highly repetitive primary structure, generalized by a three amino acid triplet: (Xaa-Yaa-Glycine), is critical for this uncommon structural assembly.Our lab has been investigating how the incorporation of aza-glycine (azGly, azG) and aza- proline (azPro, azP) residues affect the triple-helical structure and thermal stability of collagen mimetic peptides (CMPs). Although we have previously shown azGly and azPro incorporation can affect the triple-helical thermal stability of CMPs, the model systems used were quite limited in scope. Herein, the impact of azGly and azPro incorporation on CMP stability and structure is demonstrated to be dependent on a variety of different factors. This was accomplished through the synthesis of peptide libraries containing these aza-amino acids, evaluation of CMP thermal stabilities along with refolding times, and by solving high-resolution crystallographic structures of triple-helical structures. Futhermore, we optimize the synthesis of azGly-containing CMPs, evaluate the binding of azGly-containing CMPs to a target protein, and investigate an alternative CMP model system. Collectively, this body of work reports the first comprehensive set of design guidelines for incorporating azGly and azPro residues into CMPs and sets the stage for the utilization and application of aza-collagen peptides within biologically relevant systems

Apolipoprotein E is a pancreatic extracellular factor that maintains mature β-cell gene expression.

The in vivo microenvironment of tissues provides myriad unique signals to cells. Thus, following isolation, many cell types change in culture, often preserving some but not all of their in vivo characteristics in culture. At least some of the in vivo microenvironment may be mimicked by providing specific cues to cultured cells. Here, we show that after isolation and during maintenance in culture, adherent rat islets reduce expression of key β-cell transcription factors necessary for β-cell function and that soluble pancreatic decellularized matrix (DCM) can enhance β-cell gene expression. Following chromatographic fractionation of pancreatic DCM, we performed proteomics to identify soluble factors that can maintain β-cell stability and function. We identified Apolipoprotein E (ApoE) as an extracellular protein that significantly increased the expression of key β-cell genes. The ApoE effect on beta cells was mediated at least in part through the JAK/STAT signaling pathway. Together, these results reveal a role for ApoE as an extracellular factor that can maintain the mature β-cell gene expression profile

Global Surveillance of Emerging Influenza Virus Genotypes by Mass Spectrometry

Effective influenza surveillance requires new methods capable of rapid and inexpensive genomic analysis of evolving viral species for pandemic preparedness, to understand the evolution of circulating viral species, and for vaccine strain selection. We have developed one such approach based on previously described broad-range reverse transcription PCR/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) technology.Analysis of base compositions of RT-PCR amplicons from influenza core gene segments (PB1, PB2, PA, M, NS, NP) are used to provide sub-species identification and infer influenza virus H and N subtypes. Using this approach, we detected and correctly identified 92 mammalian and avian influenza isolates, representing 30 different H and N types, including 29 avian H5N1 isolates. Further, direct analysis of 656 human clinical respiratory specimens collected over a seven-year period (1999-2006) showed correct identification of the viral species and subtypes with >97% sensitivity and specificity. Base composition derived clusters inferred from this analysis showed 100% concordance to previously established clades. Ongoing surveillance of samples from the recent influenza virus seasons (2005-2006) showed evidence for emergence and establishment of new genotypes of circulating H3N2 strains worldwide. Mixed viral quasispecies were found in approximately 1% of these recent samples providing a view into viral evolution.Thus, rapid RT-PCR/ESI-MS analysis can be used to simultaneously identify all species of influenza viruses with clade-level resolution, identify mixed viral populations and monitor global spread and emergence of novel viral genotypes. This high-throughput method promises to become an integral component of influenza surveillance

OpenET : filling a critical data gap in water management for the western United States.

The lack of consistent, accurate information on evapotranspiration (ET) and consumptive use of water by irrigated agriculture is one of the most important data gaps for water managers in the western United States (U.S.) and other arid agricultural regions globally. The ability to easily access information on ET is central to improving water budgets across the West, advancing the use of data-driven irrigation management strategies, and expanding incentive-driven conservation programs. Recent advances in remote sensing of ET have led to the development of multiple approaches for field-scale ET mapping that have been used for local and regional water resource management applications by U.S. state and federal agencies. The OpenET project is a community-driven effort that is building upon these advances to develop an operational system for generating and distributing ET data at a field scale using an ensemble of six well-established satellite-based approaches for mapping ET. Key objectives of OpenET include: Increasing access to remotely sensed ET data through a web-based data explorer and data services; supporting the use of ET data for a range of water resource management applications; and development of use cases and training resources for agricultural producers and water resource managers. Here we describe the OpenET framework, including the models used in the ensemble, the satellite, meteorological, and ancillary data inputs to the system, and the OpenET data visualization and access tools. We also summarize an extensive intercomparison and accuracy assessment conducted using ground measurements of ET from 139 flux tower sites instrumented with open path eddy covariance systems. Results calculated for 24 cropland sites from Phase I of the intercomparison and accuracy assessment demonstrate strong agreement between the satellite-driven ET models and the flux tower ET data. For the six models that have been evaluated to date (ALEXI/DisALEXI, eeMETRIC, geeSEBAL, PT-JPL, SIMS, and SSEBop) and the ensemble mean, the weighted average mean absolute error (MAE) values across all sites range from 13.6 to 21.6 mm/month at a monthly timestep, and 0.74 to 1.07 mm/day at a daily timestep. At seasonal time scales, for all but one of the models the weighted mean total ET is within ±8% of both the ensemble mean and the weighted mean total ET calculated from the flux tower data. Overall, the ensemble mean performs as well as any individual model across nearly all accuracy statistics for croplands, though some individual models may perform better for specific sites and regions. We conclude with three brief use cases to illustrate current applications and benefits of increased access to ET data, and discuss key lessons learned from the development of OpenET

Three dimensional structure directs T-cell epitope dominance associated with allergy

<p>Abstract</p> <p>Background</p> <p>CD4+ T-cell epitope immunodominance is not adequately explained by peptide selectivity in class II major histocompatibility proteins, but it has been correlated with adjacent segments of conformational flexibility in several antigens.</p> <p>Methods</p> <p>The published T-cell responses to two venom allergens and two aeroallergens were used to construct profiles of epitope dominance, which were correlated with the distribution of conformational flexibility, as measured by crystallographic B factors, solvent-accessible surface, COREX residue stability, and sequence entropy.</p> <p>Results</p> <p>Epitopes associated with allergy tended to be excluded from and lie adjacent to flexible segments of the allergen.</p> <p>Conclusion</p> <p>During the initiation of allergy, the N- and/or C-terminal ends of proteolytic processing intermediates were preferentially loaded into antigen presenting proteins for the priming of CD4+ T cells.</p

Agency culture, constitutional provisions and entrepreneurship: a cross-country analysis

Substantial and systematic cross-country variation in entrepreneurship rates has been found in vari- ous studies. We attempt to explain such differences focusing on the interaction between institutional factors and population psychological characteristics. Constitutional provisions supporting economic freedom are our measure of the institutional context, whereas we proxy psychological characteristics with a country’s endowment of agency culture. We apply an IV-GMM treatment to deal with endoge- 20 neity to a data set comprising 86 countries over the period 2004–2013, and we control for de facto vari- ables and other factors that are likely to influence entrepreneurship. Our results demonstrate that agency culture is indeed an important predictor of entrepreneurship and that this effect is moderated by constitutional provisions supporting economic freedom. In particular, the impact of agency culture on entrepreneurship becomes stronger as a country expands the constitutional protection of eco- 25 nomic rights

CpG-creating mutations are costly in many human viruses.

Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses

From Duty to Right: The Role of Public Education in the Transition to Aging Societies

This paper argues that the introduction of compulsory schooling in early industrialization promoted the growth process that eventually led to a vicious cycle of population aging and negative pressure on education policy. In the early phases of industrialization, public education was undesirable for the young poor who relied on child labor. Compulsory schooling therefore discouraged childbirth, while the accompanying industrialization stimulated their demand for education. The subsequent rise in the share of the old population, however, limited government resources for education, placing heavier financial burdens on the young. This induced further fertility decline and population aging, and the resulting cycle may have delayed the growth of advanced economies in the last few decades

Scaling Production of L-Vinyglycine

L-Vinylglycine is a non-protein amino acid which has several properties that make it valuable. While L-Vinylglycine had been successfully synthesized by our group an easier, larger scale production method was desired. / / The scaled production of L-Vinylglycine was developed through experimentation regarding several key factors. The synthesis was carried out under varying conditions regarding the initial mixture of reagents, the temperature at which the primary reaction occurs, the receiving solution or lack thereof, and the retrieval of product from final reaction mixture. The synthesis was carried out using a basic distillation apparatus under a nitrogen atmosphere. / / The rate of addition of the initial reaction mixture appears to have the largest effect on the overall yield when using this method of synthesis. The rate of hydrolysis of the silyl protecting groups on the L-Vinylglycine was dramatically increased by the presence of ethanol in the receiving flask of the basic distillation apparatus used in the synthesis. Initial findings suggest the temperature at which the elimination of the sulfenic acid occurs appears to have little effect on the purity of the product when using this method. / / The success of the synthesis was primarily assessed through the yield of the product and the purity according its NMR spectra. A standard set of reaction conditions was developed, giving relatively pure L-Vinylglycine at an acceptable yield. This method could be used to easily and rapidly produce large quantities of L-Vinylglycine for further research. /