In pursuit of comparable concepts and data about collective action:

Research on collective action confronts two major obstacles. First, inconsistency in the conceptualization and operationalization of collective action, the key factors expected to affect collective action, and the outcomes of collective action hampers the accumulation of knowledge. Inconsistent terminology obscures consistent patterns. Second, the scarcity of comparable data thwarts evaluation of the relative importance of the many variables identified in the literature as likely to influence collective action. The International Forestry Resources and Institutions (IFRI) research program addresses both of these problems. Since its founding in 1993, the IFRI network of collaborating research centers has used a common set of methods and concepts to study forests, the people who use forest resources, and their institutions for resource management. The basic social unit of analysis in IFRI is the user group, defined as a set of individuals with the same rights and responsibilities to forest resources. This definition does not require formal organization or collective action, since these features are potential dependent variables. This strategy for data collection allows analysis of relationships between diverse forms of social heterogeneity and collective action within groups with comparable rights to resources. IFRI's relational database also captures the connections among forest systems, sets of resource users, particular forest products, formal and informal rules for resource use, and formal local and supra-local organizations. By the middle of 2001, the IFRI database included data on 141 sites with 231 forests, 233 user groups, 94 forest organizations, and 486 products in 12 countries. Drawing upon these data, IFRI researchers are contributing substantially to our understanding of collective action for institutional development, the mediating role institutions play relative to demographic and market pressures in patterns of resource use, and relationships between particular institutions and forest conditions. The paper describes IFRI's strategy for collecting comparable data based on consistent conceptualization and operationalization, summarizes the contributions of IFRI research to the study of collective action for natural resource management, and identifies continuing challenges.resource management, Forests and forestry Social aspects., Collective action, Forest products., Capacity,

Expansion of a chromosomal repeat in Escherichia coli: roles of replication, repair, and recombination functions

<p>Abstract</p> <p>Background</p> <p>Previous studies of gene amplification in <it>Escherichia coli </it>have suggested that it occurs in two steps: duplication and expansion. Expansion is thought to result from homologous recombination between the repeated segments created by duplication. To explore the mechanism of expansion, a 7 kbp duplication in the chromosome containing a leaky mutant version of the <it>lac </it>operon was constructed, and its expansion into an amplified array was studied.</p> <p>Results</p> <p>Under selection for <it>lac </it>function, colonies bearing multiple copies of the mutant <it>lac </it>operon appeared at a constant rate of approximately 4 to 5 per million cells plated per day, on days two through seven after plating. Expansion was not seen in a <it>recA </it>strain; null mutations in <it>recBCD </it>and <it>ruvC </it>reduced the rate 100- and 10-fold, respectively; a <it>ruvC recG </it>double mutant reduced the rate 1000-fold. Expansion occurred at an increased rate in cells lacking <it>dam</it>, <it>polA, rnhA</it>, or <it>uvrD </it>functions. Null mutations of various other cellular recombination, repair, and stress response genes had little effect upon expansion. The <it>red </it>recombination genes of phage lambda could substitute for <it>recBCD </it>in mediating expansion. In the <it>red</it>-substituted cells, expansion was only partially dependent upon <it>recA </it>function.</p> <p>Conclusion</p> <p>These observations are consistent with the idea that the expansion step of gene amplification is closely related, mechanistically, to interchromosomal homologous recombination events. They additionally provide support for recently described models of RecA-independent Red-mediated recombination at replication forks.</p

High efficiency generalized transduction in Escherichia coli O157:H7

Genetic manipulation in enterohemorrhagic E. coli O157:H7 is currently restricted to recombineering, a method that utilizes the recombination system of bacteriophage lambda, to introduce gene replacements and base changes inter alia into the genome. Bacteriophage 933W is a prophage in E. coli O157:H7 strain EDL933, which encodes the genes ( stx2AB) for the production of Shiga toxin which is the basis for the potentially fatal Hemolytic Uremic Syndrome in infected humans. We replaced the stx2AB genes with a kanamycin cassette using recombineering. After induction of the prophage by ultra-violet light, we found that bacteriophage lysates were capable of transducing to wildtype, point mutations in the lactose, arabinose and maltose genes. The lysates could also transduce tetracycline resistant cassettes. Bacteriophage 933W is also efficient at transducing markers in E. coli K-12. Co-transduction experiments indicated that the maximal amount of transferred DNA was likely the size of the bacteriophage genome, 61 kB. All tested transductants, in both E. coli K-12 and O157:H7, were kanamycin-sensitive indicating that the transducing particles contained host DNA

Chromosomal duplications and cointegrates generated by the bacteriophage lamdba Red system in Escherichia coli K-12

BACKGROUND: An Escherichia coli strain in which RecBCD has been genetically replaced by the bacteriophage λ Red system engages in efficient recombination between its chromosome and linear double-stranded DNA species sharing sequences with the chromosome. Previous studies of this experimental system have focused on a gene replacement-type event, in which a 3.5 kbp dsDNA consisting of the cat gene and flanking lac operon sequences recombines with the E. coli chromosome to generate a chloramphenicol-resistant Lac- recombinant. The dsDNA was delivered into the cell as part of the chromosome of a non-replicating λ vector, from which it was released by the action of a restriction endonuclease in the infected cell. This study characterizes the genetic requirements and outcomes of a variety of additional Red-promoted homologous recombination events producing Lac+ recombinants. RESULTS: A number of observations concerning recombination events between the chromosome and linear DNAs were made: (1) Formation of Lac+ and Lac- recombinants depended upon the same recombination functions. (2) High multiplicity and high chromosome copy number favored Lac+ recombinant formation. (3) The Lac+ recombinants were unstable, segregating Lac- progeny. (4) A tetracycline-resistance marker in a site of the phage chromosome distant from cat was not frequently co-inherited with cat. (5) Recombination between phage sequences in the linear DNA and cryptic prophages in the chromosome was responsible for most of the observed Lac+ recombinants. In addition, observations were made concerning recombination events between the chromosome and circular DNAs: (6) Formation of recombinants depended upon both RecA and, to a lesser extent, Red. (7) The linked tetracycline-resistance marker was frequently co-inherited in this case. CONCLUSIONS: The Lac+ recombinants arise from events in which homologous recombination between the incoming linear DNA and both lac and cryptic prophage sequences in the chromosome generates a partial duplication of the bacterial chromosome. When the incoming DNA species is circular rather than linear, cointegrates are the most frequent type of recombinant

A Pre-Clinical Assessment of Minocycline for Treatment of Chronic Neuropathic Pain after Spinal Cord Injury

Patients living with a spinal cord injury (SCI) often develop chronic neuropathic pain (CNP). Unfortunately, the clinically approved, current standard of treatment, gabapentin, only provides temporary pain relief. This treatment can cause numerous adverse side effects that negatively affect the daily lives of SCI patients. There is a great need for alternative, effective treatments for SCI-dependent CNP. Minocycline, an FDA-approved antibiotic, has been widely prescribed for the treatment of acne for several decades. However, recent studies demonstrate that minocycline has neuroprotective properties in several pre-clinical rodent models of CNS trauma and disease. Pre-clinical studies also show that short-term minocycline treatment can prevent the onset of CNP when delivered during the acute stage of SCI and can also transiently attenuate established CNP when delivered briefly during the chronic stage of SCI. However, the potential to abolish or attenuate CNP via long-term administration of minocycline after SCI is unknown. The purpose of this study was to investigate the potential efficacy and safety of long-term administration of minocycline to abolish or attenuate CNP following SCI. A severe spinal contusion injury was administered on adult, male, Sprague-Dawley rats. At day 29 post-injury, I initiated a three-week treatment regimen of daily administration with minocycline (50 mg/kg), gabapentin (50 mg/kg) or saline. The minocycline treatment group demonstrated a significant reduction in below-level mechanical allodynia and above- level hyperalgesia while on their treatment regimen. After a ten-day washout period of minocycline, the animals continued to demonstrate a significant reduction in below-level mechanical allodynia and above-level hyperalgesia. However, minocycline-treated animals exhibited abnormal weight gain and hepatotoxicity compared to gapabentin-treated or vehicle-treated subjects.The results support previous findings that minocycline can attenuate CNP after SCI and suggested that minocycline can also attenuate CNP via long-term delivery of minocycline after SCI (36). The data also suggested that minocycline had a lasting effect at reducing pain symptoms. However, the adverse side effects of long-term use of minocycline should not be ignored in the rodent model. Gabapentin treatment caused a significant decrease in below-level mechanical allodynia and below-level hyperalgesia during the treatment regimen. Because gabapentin treatment has an analgesic effect at the concentration I administered, the results were expected. However, I also found that gabapentin-treated animals demonstrated a sustained reduction in pain ten days after treatment withdrawal. This result was unexpected because gabapentin has a short half-life of 1.7 hours in rodents and previous studies have demonstrated that pre-drug pain levels return shortly after withdrawal of treatment. Additionally, the gabapentin-treated animals demonstrated a significant and sustained increase in rearing events compared with all other treatment groups which suggested that gabapentin treatment was not only capable of reducing pain long-term but may also significantly improve trunk stability or improve motor function recovery

Thermodynamic Prediction of Protein Neutrality

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. Our theory also predicts that a protein can gain extra robustness to the first few substitutions by increasing its thermodynamic stability. We validate our theory with simulations on lattice protein models and by showing that it quantitatively predicts previously published experimental measurements on subtilisin and our own measurements on variants of TEM1 beta-lactamase. Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications

Biotechnology manufacturing plant location decisions : Massachusetts case studies

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Urban Studies and Planning, 1993.Includes bibliographical references (leaves 111-114).by Jean S. Poteete.M.S

Wicked but worth it: student perspectives on socio-hydrology

harvestPolicy AnalysisMulti Actor System

Is commoning compatible with heterotopia? Reflections from Montreal's Champ des Possibles

Heterotopic green spaces enhance urban regeneration more than other urban green spaces, precisely because of their informality, diversity of activities and imaginings, marginality, and dynamism (cf., Stavrides 2007). Bottom-up occupation of and informal claims to urban space transform relations among people and space. “Commoning” occurs when these transformations produce shared access to and maintenance of resources and/or spaces combined with a sense of mutuality among participants (Bollier and Helfrich 2015, 2019; Blomley 2008, 2016; Linebaugh 2008, 79, 279; Williams 2018). Commoning contributes to the vitality and durability of bottom-up efforts to reclaim and share spaces and resources (Gibson-Graham 2006; Ostrom 1990; Singh 2017). But is it also compatible with heterotopia? In principle, commoning could facilitate coexistence, but if there are tensions among varied imaginaries and activities, it may be incompatible with heterotopia (cf., Helton 2015; Nightingale 2018; Velicu & García-López 2018). We explore these questions in the context of Montreal’s Champ des Possibles, an abandoned railyard that has transformed into an open urban green space where an eclectic and changing set of people engage in a wide variety of activities. Observations and narratives from the Champ des Possible suggest that, despite many tensions and sources of incompatibility, heterotopia and commoning can coexist. The scale, discretion, ephemerality, and tendency to foreclose or open possibilities of activities, values, and visions associated with heterotopia and commoning influence their social acceptability, and thus their compatibility. Our case material also suggests, however, that the question does not fully capture the dynamism or complexity of heterotopia and commoning