Harmonization and standardization of nucleus pulposus cell extraction and culture methods

Background In vitro studies using nucleus pulposus (NP) cells are commonly used to investigate disc cell biology and pathogenesis, or to aid in the development of new therapies. However, lab-to-lab variability jeopardizes the much-needed progress in the field. Here, an international group of spine scientists collaborated to standardize extraction and expansion techniques for NP cells to reduce variability, improve comparability between labs and improve utilization of funding and resources. Methods The most commonly applied methods for NP cell extraction, expansion, and re-differentiation were identified using a questionnaire to research groups worldwide. NP cell extraction methods from rat, rabbit, pig, dog, cow, and human NP tissue were experimentally assessed. Expansion and re-differentiation media and techniques were also investigated. Results Recommended protocols are provided for extraction, expansion, and re-differentiation of NP cells from common species utilized for NP cell culture. Conclusions This international, multilab and multispecies study identified cell extraction methods for greater cell yield and fewer gene expression changes by applying species-specific pronase usage, 60–100 U/ml collagenase for shorter durations. Recommendations for NP cell expansion, passage number, and many factors driving successful cell culture in different species are also addressed to support harmonization, rigor, and cross-lab comparisons on NP cells worldwide

Does Transparency Pay?

This paper studies whether transparency (measured by accuracy and frequency of macroeconomic information released to the public) leads to lower borrowing costs in sovereign bond markets. We analyze the data generated during 1999–2002 when the International Monetary Fund (IMF) instituted new ways for countries to increase their transparency—by publishing the IMF's assessment of their policies and committing to release more accurate data more frequently. The IMF's preexisting internal timetable for country reports introduced exogenous variation when countries were faced with the option to become more transparent. We exploit this time variation and construct instruments to estimate the impact of transparency on bond yields in a way that is free from endogeneity bias. We find that countries experience a statistically significant decline in borrowing costs (11 percent reduction in credit spreads on average) when they choose to become more transparent. The magnitude of the decline is inversely related to the initial level of transparency and the size of the debt market. IMF Staff Papers (2007) 55, 183–209; doi:10.1057/palgrave.imfsp.9450028; published online 22 January 2008

Quality of life in the economic and urban economic literature

Quality of life (QoL) is increasingly becoming a concept researched empirically and theoretically in the field of economics. In urban economics in particular, this increasing interest stems mainly from the fact that QoL affects urban competitiveness and urban growth: research shows that when households and businesses decide where to locate, QoL considerations can play a very important role. The purpose of the present paper is to examine the way economic literature and urban economic literature in particular, have adopted QoL considerations in the economic thinking. Moreover, it presents the ways various studies have attempted to capture the multidimensional nature of the concept, and quantify it for the purposes of empirical research. Conclusions are drawn on the state of affairs regarding the study of QoL in economics, as well as the problems of measurement arising mainly from the complex nature of the concept

Entry costs and cross-country differences in productivity and output

Entry costs, Entry regulation, Entry barriers, Institutions, Productivity, TFP, O11, O17,

Strategic institutional choice: Voters, states, and congressional term limits

States’ choices on term limits are quantified as a multiple-categorical variable capturing variation in the type of limits passed. Measures of relative political influence in Congress explain much of this variation. Using 1992 data on the American states, the model controls for unobserved heterogeneity due to voter access to direct democracy in some states. At 2002 values for congressional tenure and federal spending, the model predicts approximately eight to ten additional states would choose to limit their own members’ terms but cannot under a Supreme Court ruling. We discuss implications for institutional federalism and the potential passage of similar political institutions across the states. Copyright Springer Science+Business Media, LLC 2007Term limits, Political institutions, Federalism, Political economy,

Protein complex analysis project (PCAP): Project overview

The Protein Complex Analysis Project (PCAP) has two major goals: 1. to develop an integrated set of high throughput pipelines to identify and characterize multi-protein complexes in a microbe more swiftly and comprehensively than currently possible and 2. to use these pipelines to elucidate and model the protein interaction networks regulating stress responses in Desulfovibrio vulgaris with the aim of understanding how this and similar microbes can be used in bioremediation of metal and radionuclides found in U.S. Department of Energy (DOE) contaminated sites. PCAP builds on the established research and infrastructure of another Genomics: GTL initiative conducted by the Environmental Stress Pathways Project (ESPP). ESPP has developed D. vulgaris as a model for stress responses and has used gene expression profiling to define specific sets of proteins whose expression changes after application of a stressor. Proteins, however, do not act in isolation. They participate in intricate networks of protein/protein interactions that regulate cellular metabolism. To understand and model how these identified genes affect the organism, therefore, it is essential to establish not only the other proteins that they directly contact, but the full repertoire of protein/protein interactions within the cell. In addition, there may well be genes whose activity is changed in response to stress not by regulating their expression level but by altering the protein partners that they bind, by modifying their structures, or by changing their subcellular locations. There may also be differences in the way proteins within individual cells respond to stress that are not apparent in assays that examine the average change in a population of cells. Therefore, we are extending ESPP's analysis to characterize the polypeptide composition of as many multi-protein complexes in the cell as possible and determine their stoichiometries, their quaternary structures, and their locations in planktonic cells and in individual cells within biofilms. PCAP will characterize complexes in wild type cells grown under normal conditions and also examine how these complexes are affected in cells perturbed by stress or by mutation of key stress regulatory genes. These data will all be combined with those of the ongoing work of the ESPP to understand, from a physical-chemical, control-theoretical, and evolutionary point of view, the role of multi-protein complexes in stress pathways involved in the biogeochemistry of soil microbes under a wide variety of conditions. Essential to this endeavor is the development of automated high throughput methods that are robust and allow for the comprehensive analysis of many protein complexes. Biochemical purification of endogenous complexes and identification by mass spectrometry is being coupled with in vitro and in vivo EM molecular imaging methods. Because no single method can isolate all complexes, we are developing two protein purification pipelines, one the current standard Tandem Affinity Purification approach, the other a novel tagless strategy. Specific variants ofeach of these are being developed for water soluble and membrane proteins. Our Bioinstrumentation group is developing highly parallel micro-scale protein purification and protein sample preparation platforms, and mass spectrometry data analysis is being automated to allow the throughput required. The stoichiometries of the purified complexes are being determined and the quaternary structures of complexes larger than 250 kDa are being solved by single particle EM. We are developing EM tomography approaches to examine whole cells and sectioned, stained material to detect complexes in cells and determine their localization and structures. New image analysis methods will be applied to speed determination of quaternary structures from EM data. Once key components in the interaction network are defined, to test and validate our pathway models, mutant strains not expressing thes