TILLING for Mutations in Model Plants and Crops

A growing world population, changing climate and limiting fossil fuels will provide new pressures on human production of food, medicine, fuels and feed stock in the twenty-first century. Enhanced crop production promises to ameliorate these pressures. Crops can be bred for increased yields of calories, starch, nutrients, natural medicinal compounds, and other important products. Enhanced resistance to biotic and abiotic stresses can be introduced, toxins removed, and industrial qualities such as fibre strength and biofuel per mass can be increased. Induced and natural mutations provide a powerful method for the generation of heritable enhanced traits. While mainly exploited in forward, phenotype driven, approaches, the rapid accumulation of plant genomic sequence information and hypotheses regarding gene function allows the use of mutations in reverse genetic approaches to identify lesions in specific target genes. Such gene-driven approaches promise to speed up the process of creating novel phenotypes, and can enable the generation of phenotypes unobtainable by traditional forward methods. TILLING (Targeting Induced Local Lesions IN Genome) is a high-throughput and low cost reverse genetic method for the discovery of induced mutations. The method has been modified for the identification of natural nucleotide polymorphisms, a process called Ecotilling. The methods are general and have been applied to many species, including a variety of different crops. In this chapter the current status of the TILLING and Ecotilling methods and provide an overview of progress in applying these methods to different plant species, with a focus on work related to food production for developing nations.

Quantification of oxidized levels of specific RNA species using an aldehyde reactive probe

Emerging evidence has shown that oxidation of RNA, including messenger RNA (mRNA), is elevated in several age-related diseases, although investigation of oxidized levels of individual RNA species has been limited. Recently we reported that an aldehyde reactive probe (ARP) quantitatively reacts with oxidatively modified depurinated/depyrimidinated (abasic) RNA. Here we report a novel method to isolate oxidized RNA using ARP and streptavidin beads. An oligo RNA containing abasic sites that were derivatized with ARP was pulled down by streptavidin beads, whereas a control oligo RNA was not. In vitro oxidized RNA, as well as total cellular RNA, isolated from oxidatively stressed cells was also pulled down, dependent on oxidation level, and concentrated in the pull-down fraction. Quantitative reverse transcription polymerase chain reaction (RT-PCR) using RNA in the pull-down fraction demonstrated that several gene transcripts were uniquely increased in the fraction by oxidative stress. Thus, our method selectively concentrates oxidized RNA by pull-down and enables the assessment of oxidation levels of individual RNA species. (C) 2011 Elsevier Inc. All rights reserved.

Predictors of sickness absence in patients with a new episode of low back pain in primary care

This study examines predictors of sickness absence in patients presenting to a health practitioner with acute/ subacute low back pain (LBP). Aims of this study were to identify baseline-variables that detect patients with a new LBP episode at risk of sickness absence and to identify prognostic models for sickness absence at different time points after initial presentation. Prospective cohort study investigating 310 patients presenting to a health practitioner with a new episode of LBP at baseline, three-, six-, twelve-week and six-month follow-up, addressing work-related, psychological and biomedical factors. Multivariate logistic regression analysis was performed to identify baseline-predictors of sickness absence at different time points. Prognostic models comprised 'job control', 'depression' and 'functional limitation' as predictive baseline-factors of sickness absence at three and six-week follow-up with 'job control' being the best single predictor (OR 0.47; 95%CI 0.26-0.87). The six-week model explained 47% of variance of sickness absence at six-week follow-up (p<0.001). The prediction of sickness absence beyond six-weeks is limited, and health practitioners should re-assess patients at six weeks, especially if they have previously been identified as at risk of sickness absence. This would allow timely intervention with measures designed to reduce the likelihood of prolonged sickness absence.

Experience with a gravitational valve in the management of symptomatic overdrainage in children with shunts

Symptomatic overdrainage in children with shunt-treated hydrocephalus represents one of the more difficult shunt-related diseases and may require repeated surgery. Gravity-assisted valve design has become a standard device to avoid overdrainage in many European pediatric hydrocephalus centers. However, the use of a gravitational valve for relieving symptoms associated with overdrainage has not yet been addressed. The goal of this study was to evaluate the effectiveness of a gravitational valve in the treatment of symptomatic overdrainage in children with shunts.

[Pulmonary hypertension and lung edema at high altitude. Role of endothelial dysfunction and fetal programming]

High altitude constitutes an exciting natural laboratory for medical research. While initially, the aim of high-altitude research was to understand the adaptation of the organism to hypoxia and find treatments for altitude-related diseases, over the past decade or so, the scope of this research has broadened considerably. Two important observations led to the foundation for the broadening of the scientific scope of high-altitude research. First, high-altitude pulmonary edema (HAPE) represents a unique model which allows studying fundamental mechanisms of pulmonary hypertension and lung edema in humans. Secondly, the ambient hypoxia associated with high-altitude exposure facilitates the detection of pulmonary and systemic vascular dysfunction at an early stage. Here, we review studies that, by capitalizing on these observations, have led to the description of novel mechanisms underpinning lung edema and pulmonary hypertension and to the first direct demonstration of fetal programming of vascular dysfunction in humans.

Assessment Of Dynamic Properties Of A Crowd Model For Human-Structure Interaction Modeling

As lightweight and slender structural elements are more frequently used in the design, large scale structures become more flexible and susceptible to excessive vibrations. To ensure the functionality of the structure, dynamic properties of the occupied structure need to be estimated during the design phase. Traditional analysis method models occupants simply as an additional mass; however, research has shown that human occupants could be better modeled as an additional degree-of- freedom. In the United Kingdom, active and passive crowd models are proposed by the Joint Working Group as a result of a series of analytical and experimental research. It is expected that the crowd models would yield a more accurate estimation to the dynamic response of the occupied structure. However, experimental testing recently conducted through a graduate student project at Bucknell University indicated that the proposed passive crowd model might be inaccurate in representing the impact on the structure from the occupants. The objective of this study is to provide an assessment of the validity of the crowd models proposed by JWG through comparing the dynamic properties obtained from experimental testing data and analytical modeling results. The experimental data used in this study was collected by Firman in 2010. The analytical results were obtained by performing a time-history analysis on a finite element model of the occupied structure. The crowd models were created based on the recommendations from the JWG combined with the physical properties of the occupants during the experimental study. During this study, SAP2000 was used to create the finite element models and to implement the analysis; Matlab and ME¿scope were used to obtain the dynamic properties of the structure through processing the time-history analysis results from SAP2000. The result of this study indicates that the active crowd model could quite accurately represent the impact on the structure from occupants standing with bent knees while the passive crowd model could not properly simulate the dynamic response of the structure when occupants were standing straight or sitting on the structure. Future work related to this study involves improving the passive crowd model and evaluating the crowd models with full-scale structure models and operating data.

Changes in Psychological Characteristics of Working Adults in Different Stages of Economic Transition in Lithuania

Global economic changes have psychological consequences and Mr. Lepeska set out to assess these changes in working adults in Lithuania between 1993 and 1997. He surveyed two groups of working adults, with a total of 200 people, randomly selected and representing different organisations and professions. In both groups around 30% of participants were managers, with the remainder working in non-managerial positions. The participants were surveyed twice, once in 1993 and the second time in 1997,using various psychodiagnostic tools to measure their psychological characteristics. The results showed that strategies for coping with stress have changed, with problem solving strategies being used more often, and avoidance behaviour or seeking social support less. Men tended to have rejected these strategy more radically than women. Attitudes towards work had become more positive, with managers' attitudes having changed more significantly than those of employees from lower levels of organisations. Younger people were more positive towards work-related changes, while situational anxiety tended to increase with age, although overall it remained low. Mr. Lepeska found that while there were some indications of an increasing individualist in relation to peers, the traditional collective orientation of Lithuanian adults had if anything increased. People have become more accepting of an unequal distribution of power, making it difficult to increase the participation of subordinates in decision making. He also noted a tendency for Lithuanians to see their organisations as traditional families, expecting them to take care of them physically and economically in return for loyalty. The strong feminine orientation with its stress on interpersonal relations and overall quality of life has also strengthened, but the ability of Lithuanians to take initiative and control their environment was relatively low. Mr. Lepeska concludes that organisations should seek to recruit people who are able to adjust more easily to changes and consider measuring dominance, individualism, and attitudes to work-related change and situational anxiety in the process of professional selection. There should also be more emphasis on team building and on training managers to maintain closer relationships with their subordinates so as to increase the latter's participation in decision making. Good interpersonal relations can be a strong work motivator, as may be special attention to the security needs of older employees.

A qualitative study on the role of cultural background in patients perspectives on rehabilitation

Background Low back pain (LBP) is one of the major concerns in health care. In Switzerland, musculoskeletal problems represent the third largest illness group with 9.4 million consultations per year. The return to work rate is increased by an active treatment program and saves societal costs. However, results after rehabilitation are generally poorer in patients with a Southeast European cultural background than in other patients. This qualitative research about the rehabilitation of patients with LBP and a Southeast European cultural background, therefore, explores possible barriers to successful rehabilitation. Methods We used a triangulation of methods combining three qualitative methods of data collection: 13 semi-structured in-depth interviews with patients who have a Southeast European cultural background and live in Switzerland, five semi-structured in-depth interviews and two focus groups with health professionals, and a literature review. Between June and December 2008, we recruited participants at a Rehabilitation Centre in the German-speaking part of Switzerland. Results To cope with pain, patients prefer passive strategies, which are not in line with recommended coping strategies. Moreover, the families of patients tend to support passive behaviour and reduce the autonomy of patients. Health professionals and researchers propagate active strategies including activity in the presence of pain, yet patients do not consider psychological factors contributing to LBP. The views of physicians and health professionals are in line with research evidence demonstrating the importance of psychosocial factors for LBP. Treatment goals focusing on increasing daily activities and return to work are not well understood by patients partly due to communication problems, which is something that patients and health professionals are aware of. Additional barriers to returning to work are caused by poor job satisfaction and other work-related factors. Conclusions LBP rehabilitation can be improved by addressing the following points. Early management of LBP should be activity-centred instead of pain-centred. It is mandatory to implement return to work management early, including return to adapted work, to improve rehabilitation for patients. Rehabilitation has to start when patients have been off work for three months. Using interpreters more frequently would improve communication between health professionals and patients, and reduce misunderstandings about treatment procedures. Special emphasis must be put on the process of goal-formulation by spending more time with patients in order to identify barriers to goal attainment. Information on the return to work process should also include the financial aspects of unemployment and disability.

Occupational maxillofacial fractures: a 3-year survey in central Switzerland

PURPOSE: The aim of this study was to determine occupational facial fractures in central Switzerland. Concomitant injuries were also studied. MATERIALS AND METHODS: The Department of Cranio-Maxillofacial Surgery at the University Hospital in Berne provides a 24-hour maxillofacial trauma service for its population (1.6 million). The present study was comprised of 42 patients (8.4% of treated maxillofacial injuries) with occupational maxillofacial fractures registered at this unit between 2000 and 2002. Information on the topic of occupation, the cause of the accidents, and the topographic location of the fractures was analyzed. RESULTS: The mean age of the patients was 44.4 years, with a male to female ratio of 41:1. Sixty-nine percent of the injuries occurred in farm and forestry workers and in construction laborers during the summertime (33%). Workers in these occupations carried a 127-fold (farm and forestry workers) and a 44-fold (construction laborers) higher risk of incurring maxillofacial fractures than did service and office workers. Injuries were most frequently (43%) caused by a thrown, projected, or falling object. Eighty-two percent of the fractures occurred in the midface region and at the skull base. Fifty-nine percent of the patients had concomitant injuries. In 69%, surgery was necessary, the mean duration of their hospital stay being 4.8 days. CONCLUSION: The probability of sustaining work-related maxillofacial traumata is correlated to the nature of the occupation. Farm and forestry workers are at the highest risk, most frequently injured by being struck by an object or an animal. The introduction of personalized safety measures should become obligatory in high-risk occupations.

Preparing writing centers and tutors for literacy mediation for working class campus-staff

Writing centers work with writers; traditionally services have been focused on undergraduates taking composition classes. More recently, centers have started to attract a wider client base including: students taking labs that require writing; graduate students; and ESL students learning the conventions of U.S. communication. There are very few centers, however, which identify themselves as open to working with all members of the campus-community. Michigan Technological University has one such center. In the Michigan Tech writing center, doors are open to “all students, faculty and staff.” While graduate students, post docs, and professors preparing articles for publication have used the center, for the first time in the collective memory of the center UAW staff members requested center appointments in the summer of 2008. These working class employees were in the process of filling out a work related document, the UAW Position Audit, an approximately seven-page form. This form was their one avenue for requesting a review of the job they were doing; the review was the first step in requesting a raise in job level and pay. This study grew out of the realization that implicit literacy expectations between working class United Auto Workers (UAW) staff and professional class staff were complicating the filling out and filing of the position audit form. Professional class supervisors had designed the form as a measure of fairness, in that each UAW employee on campus was responding to the same set of questions about their work. However, the implicit literacy expectations of supervisors were different from those of many of the employees who were to fill out the form. As a result, questions that were meant to be straightforward to answer were in the eyes of the employees filling out the form, complex. Before coming to the writing center UAW staff had spent months writing out responses to the form; they expressed concerns that their responses still would not meet audience expectations. These writers recognized that they did not yet know exactly what the audience was expecting. The results of this study include a framework for planning writing center sessions that facilitate the acquisition of literacy practices which are new to the user. One important realization from this dissertation is that the social nature of literacy must be kept in the forefront when both planning sessions and when educating tutors to lead these sessions. Literacy scholars such as James Paul Gee, Brian Street, and Shirley Brice Heath are used to show that a person can only know those literacy practices that they have previously acquired. In order to acquire new literacy practices, a person must have social opportunities for hands-on practice and mentoring from someone with experience. The writing center can adapt theory and practices from this dissertation that will facilitate sessions for a range of writers wishing to learn “new” literacy practices. This study also calls for specific changes to writing center tutor education.

Differences across health care systems in outcome and cost-utility of surgical and conservative treatment of chronic low back pain: a study protocol

BACKGROUND: There is little evidence on differences across health care systems in choice and outcome of the treatment of chronic low back pain (CLBP) with spinal surgery and conservative treatment as the main options. At least six randomised controlled trials comparing these two options have been performed; they show conflicting results without clear-cut evidence for superior effectiveness of any of the evaluated interventions and could not address whether treatment effect varied across patient subgroups. Cost-utility analyses display inconsistent results when comparing surgical and conservative treatment of CLBP. Due to its higher feasibility, we chose to conduct a prospective observational cohort study. METHODS: This study aims to examine if1. Differences across health care systems result in different treatment outcomes of surgical and conservative treatment of CLBP2. Patient characteristics (work-related, psychological factors, etc.) and co-interventions (physiotherapy, cognitive behavioural therapy, return-to-work programs, etc.) modify the outcome of treatment for CLBP3. Cost-utility in terms of quality-adjusted life years differs between surgical and conservative treatment of CLBP.This study will recruit 1000 patients from orthopaedic spine units, rehabilitation centres, and pain clinics in Switzerland and New Zealand. Effectiveness will be measured by the Oswestry Disability Index (ODI) at baseline and after six months. The change in ODI will be the primary endpoint of this study.Multiple linear regression models will be used, with the change in ODI from baseline to six months as the dependent variable and the type of health care system, type of treatment, patient characteristics, and co-interventions as independent variables. Interactions will be incorporated between type of treatment and different co-interventions and patient characteristics. Cost-utility will be measured with an index based on EQol-5D in combination with cost data. CONCLUSION: This study will provide evidence if differences across health care systems in the outcome of treatment of CLBP exist. It will classify patients with CLBP into different clinical subgroups and help to identify specific target groups who might benefit from specific surgical or conservative interventions. Furthermore, cost-utility differences will be identified for different groups of patients with CLBP. Main results of this study should be replicated in future studies on CLBP.

Functions and effects of creatine in the central nervous system

Creatine kinase catalyses the reversible transphosphorylation of creatine by ATP. In the cell, creatine kinase isoenzymes are specifically localized at strategic sites of ATP consumption to efficiently regenerate ATP in situ via phosphocreatine or at sites of ATP generation to build-up a phosphocreatine pool. Accordingly, the creatine kinase/phosphocreatine system plays a key role in cellular energy buffering and energy transport, particularly in cells with high and fluctuating energy requirements like neurons. Creatine kinases are expressed in the adult and developing human brain and spinal cord, suggesting that the creatine kinase/phosphocreatine system plays a significant role in the central nervous system. Functional impairment of this system leads to a deterioration in energy metabolism, which is phenotypic for many neurodegenerative and age-related diseases. Exogenous creatine supplementation has been shown to reduce neuronal cell loss in experimental paradigms of acute and chronic neurological diseases. In line with these findings, first clinical trials have shown beneficial effects of therapeutic creatine supplementation. Furthermore, creatine was reported to promote differentiation of neuronal precursor cells that might be of importance for improving neuronal cell replacement strategies. Based on these observations there is growing interest on the effects and functions of this compound in the central nervous system. This review gives a short excursion into the basics of the creatine kinase/phosphocreatine system and aims at summarizing findings and concepts on the role of creatine kinase and creatine in the central nervous system with special emphasis on pathological conditions and the positive effects of creatine supplementation.

Development of an optimization model for biofuel facility size and location and a simulation model for design of a biofuel supply chain

To mitigate greenhouse gas (GHG) emissions and reduce U.S. dependence on imported oil, the United States (U.S.) is pursuing several options to create biofuels from renewable woody biomass (hereafter referred to as “biomass”). Because of the distributed nature of biomass feedstock, the cost and complexity of biomass recovery operations has significant challenges that hinder increased biomass utilization for energy production. To facilitate the exploration of a wide variety of conditions that promise profitable biomass utilization and tapping unused forest residues, it is proposed to develop biofuel supply chain models based on optimization and simulation approaches. The biofuel supply chain is structured around four components: biofuel facility locations and sizes, biomass harvesting/forwarding, transportation, and storage. A Geographic Information System (GIS) based approach is proposed as a first step for selecting potential facility locations for biofuel production from forest biomass based on a set of evaluation criteria, such as accessibility to biomass, railway/road transportation network, water body and workforce. The development of optimization and simulation models is also proposed. The results of the models will be used to determine (1) the number, location, and size of the biofuel facilities, and (2) the amounts of biomass to be transported between the harvesting areas and the biofuel facilities over a 20-year timeframe. The multi-criteria objective is to minimize the weighted sum of the delivered feedstock cost, energy consumption, and GHG emissions simultaneously. Finally, a series of sensitivity analyses will be conducted to identify the sensitivity of the decisions, such as the optimal site selected for the biofuel facility, to changes in influential parameters, such as biomass availability and transportation fuel price. Intellectual Merit The proposed research will facilitate the exploration of a wide variety of conditions that promise profitable biomass utilization in the renewable biofuel industry. The GIS-based facility location analysis considers a series of factors which have not been considered simultaneously in previous research. Location analysis is critical to the financial success of producing biofuel. The modeling of woody biomass supply chains using both optimization and simulation, combing with the GIS-based approach as a precursor, have not been done to date. The optimization and simulation models can help to ensure the economic and environmental viability and sustainability of the entire biofuel supply chain at both the strategic design level and the operational planning level. Broader Impacts The proposed models for biorefineries can be applied to other types of manufacturing or processing operations using biomass. This is because the biomass feedstock supply chain is similar, if not the same, for biorefineries, biomass fired or co-fired power plants, or torrefaction/pelletization operations. Additionally, the research results of this research will continue to be disseminated internationally through publications in journals, such as Biomass and Bioenergy, and Renewable Energy, and presentations at conferences, such as the 2011 Industrial Engineering Research Conference. For example, part of the research work related to biofuel facility identification has been published: Zhang, Johnson and Sutherland [2011] (see Appendix A). There will also be opportunities for the Michigan Tech campus community to learn about the research through the Sustainable Future Institute.