AGOS: A Plug-and-Play Method for the Assembly of Artificial Gene Operons into Functional Biosynthetic Gene Clusters

The generation of novel secondary metabolites by reengineering or refactoring biochemical pathways is a rewarding but also challenging goal of synthetic biology. For this, the development of tools for the reconstruction of secondary metabolite gene clusters as well as the challenge of understanding the obstacles in this process is of great interest. The artificial gene operon assembly system (AGOS) is a plug-and-play method developed as a tool to consecutively assemble artificial gene operons into a destination vector and subsequently express them under the control of a de-repressed promoter in a Streptomyces host strain. AGOS was designed as a set of entry plasmids for the construction of artificial gene operons and a SuperCos1 based destination vector, into which the constructed operons can be assembled by Red/ET-mediated recombination. To provide a proof-of-concept of this method, we disassembled the well-known novobiocin biosynthetic gene cluster into four gene operons, encoding for the different moieties of novobiocin. We then genetically reorganized these gene operons with the help of AGOS to finally obtain the complete novobiocin gene cluster again. The production of novobiocin precursors and of novobiocin could successfully be detected by LC-MS and LC-MS/MS. Furthermore, we demonstrated that the omission of terminator sequences only had a minor impact on product formation in our system.

Pollen-based quantitative reconstructions of Holocene regional vegetation cover (plant-functional types and land-cover types) in Europe suitable for climate modelling

We present quantitative reconstructions of regional vegetation cover in north-western Europe, western Europe north of the Alps, and eastern Europe for five time windows in the Holocene [around 6k, 3k, 0.5k, 0.2k, and 0.05k calendar years before present (bp)] at a 1° × 1° spatial scale with the objective of producing vegetation descriptions suitable for climate modelling. The REVEALS model was applied on 636 pollen records from lakes and bogs to reconstruct the past cover of 25 plant taxa grouped into 10 plant-functional types and three land-cover types [evergreen trees, summer-green (deciduous) trees, and open land]. The model corrects for some of the biases in pollen percentages by using pollen productivity estimates and fall speeds of pollen, and by applying simple but robust models of pollen dispersal and deposition. The emerging patterns of tree migration and deforestation between 6k bp and modern time in the REVEALS estimates agree with our general understanding of the vegetation history of Europe based on pollen percentages. However, the degree of anthropogenic deforestation (i.e. cover of cultivated and grazing land) at 3k, 0.5k, and 0.2k bp is significantly higher than deduced from pollen percentages. This is also the case at 6k in some parts of Europe, in particular Britain and Ireland. Furthermore, the relationship between summer-green and evergreen trees, and between individual tree taxa, differs significantly when expressed as pollen percentages or as REVEALS estimates of tree cover. For instance, when Pinus is dominant over Picea as pollen percentages, Picea is dominant over Pinus as REVEALS estimates. These differences play a major role in the reconstruction of European landscapes and for the study of land cover-climate interactions, biodiversity and human resources.

Holocene biomass burning and global dynamics of the carbon cycle

Fire regimes have changed during the Holocene due to changes in climate, vegetation, and in human practices. Here, we hypothesise that changes in fire regime may have affected the global CO2 concentration in the atmosphere through the Holocene. Our data are based on quantitative reconstructions of biomass burning deduced from stratified charcoal records from Europe, and South-, Central- and North America, and Oceania to test the fire-carbon release hypothesis. In Europe the significant increase of fire activity is dated approximately 6000 cal. yr ago. In north-eastern North America burning activity was greatest before 7500 years ago, very low between 7500-3000 years, and has been increasing since 3000 years ago. In tropical America, the pattern is more complex and apparently latitudinally zonal. Maximum burning occurred in the southern Amazon basin and in Central America during the middle Holocene, and during the last 2000 years in the northern Amazon basin. In Oceania, biomass burning has decreased since a maximum 5000 years ago. Biomass burning has broadly increased in the Northern and Southern hemispheres throughout the second half of the Holocene associated with changes in climate and human practices. Global fire indices parallel the increase of atmospheric CO2 concentration recorded in Antarctic ice cores. Future issues on carbon dynamics relatively to biomass burning are discussed to improve the quantitative reconstructions.

[Infected animal bite injuries of the extremities]

The appearance of animal bite injuries varies in regard to location and extent. Injuries with puncture wounds involving the extremities carry great risk of infection. Managing the complications often requires substantial medical treatment and increased costs. The aim of this study is the evaluation of the course of disease, medical care, and treatment costs in patients with infected bite injuries. In the year 2000, 16 patients were treated for infection after bite injuries of the extremities. Fourteen patients received substandard therapy because of incorrect assessment of the extent of the bite wound. Because of infection, the average time needed for treatment before returning to work was 3 months, including 12 days of hospitalization and 16 days of out-patient treatment. The average treatment costs exceeded 6,100 Euro for the health insurance companies. Because of its increasing prevalence and inadequate treatment, this type of injury has become a serious public health problem.

[Cost measurement based on a cost diary in patients with inflammatory bowel disease]

OBJECTIVE

Cost diaries administered by patients have been used as a method to measure costs for different diseases. Our aim was to test the application of a patient cost diary in patients with inflammatory bowel disease (IBD) and to measure disease specific resource utilization and costs.

PATIENTS AND METHODS

A specific patient cost diary for IBD was developed and tested in a prospective pilot study. 105 outpatients with IBD of a University Hospital agreed to participate over a 4 week follow-up period. They were asked to report weekly their use of medical care and costs related to their illness. Visits to health care providers, hospitalizations, drug use, costs due to absence from paid and unpaid work, travel costs as well as out-of-pocket expenses were considered.

RESULTS

The response rate was 90 %. Almost 70 % of the patients estimated the diary as easy to fill in. Compared with other data sources, the cost measurement using the cost diary showed good agreement regarding costs of drug therapy and outpatient hospital treatment. Mean costs due to illness were estimated to be 1,500 Euro per 4 weeks. This corresponds to total costs of about 20,000 Euro per year of care. 69 % of total costs were indirect costs due to illness-related absence from work, days of inactivity at home, and early retirement. Direct health care and direct non health care costs (e. g. travel costs) were responsible for 27 % and 4 % of costs, respectively.

DISCUSSION AND CONCLUSION

The presented instrument offers a suitable and practical method of assessing IBD-related resource utilization. The prospectively obtained data for direct medical and non medical, as well as indirect costs allow a cost measurement from the societal perspective. The presented cost diary can be used for measuring costs for economic evaluations of medical interventions.

[Radiologic diagnosis of fistulas and abscesses in Crohn's disease: cost-effectiveness analysis of 2 different imaging strategies]

PURPOSE

To analyze cost-effectiveness of magnetic resonance imaging and conventional enteroclysis in the assessment of fistulas and abscesses in patients with Crohn's disease (CD).

METHODS

A decision analytic model was used to compare enteroclysis with MRI, performing a cost-effectiveness analysis of both diagnostic strategies. Data from 84 patients undergoing a clinical trial were used. Primary outcome was defined as one correctly diagnosed patient regarding Crohn's disease, fistulas, and abscesses, including true-positive and true-negative cases. Costs of the two procedures were estimated in German Marks (DM) using fee schedules. The influence of different definitions of effects was calculated. For all variables single and multiple sensitivity analyses were performed.

RESULTS

Incremental cost effectiveness of MRI vs. enteroclysis was 3,119.33 DM per one additional correctly diagnosed patient. The results of sensitivity analyses suggest that MRI use in certain patient subgroups (patients at higher prevalence of CD, fistulas, and abscesses) even becomes more cost-effective. In this case one additional effect could be gained below 1,650 DM.

CONCLUSIONS

From an economic perspective, decision makers should consider the use of MRI in the work-up of patients with Crohn's disease as an efficient procedure under certain conditions. To support treatment policies for physicians or insurance coverage of certain diagnostic strategies the costs possibly saved with MRI should also be considered.

[Development and validation of a prognosis model for predicting work capacity after rehabilitation based on routinely collected parameters]

For efficient rehabilitation it is important to identify, as early as possible, the patients likely to be successfully returned to work after rehabilitation. The aim of this pilot study was to develop a statistical model for predicting this return as reliably as possible. The model uses only information readily available at the beginning of rehabilitation. A multiple regression analysis with backward elimination was used from a routine data base and identified 8 variables of prognostic value. The model offers a comfortable possibility to predict the probability of return to work of a patient on the basis of routinely registered data. The prognosis was found correct in 68% of those returning to work after rehabilitation (sensitivity) and in 80% of those who did not (specificity). Further work to improve the model for prognosis in rehabilitation research is considered reasonable.

[Clinical studies in rehabilitation research--problems and solutions from biometrical perspective]

Methodology of clinical studies is highly sophisticated in drug research. But clinical trials are also necessary to demonstrate efficacy and safety of rehabilitation treatment. The call for evidence based medicine has also reached rehabilitation. However, in rehabilitation medicine it is much more difficult to design and conduct clinical trials with a high methodological standard. Among the reasons are: A comparable control group is necessary because spontaneous healing and unspecific measures contribute to therapeutic success, too. But what could "placebo rehabilitation" look like? The masking of therapies (blinded studies) will hardly ever be possible. Therefore, it is more difficult to achieve the same treatment and observation for the treatment and control group. Treatments in rehabilitation take longer to become effective than a drug and maybe the success will disappear after some time. Therefore, long-term trials and follow-ups are necessary. Such studies are expensive, need a strong organisation, and drop-outs are unavoidable. An appropriate outcome variable does not always exist. "Return to work" is an important, reliable and valid variable, but it delivers only one bit of information per patient. As a consequence, smaller progress in rehabilitation can only be demonstrated with large sample sizes. Outcome variables based on time enable studies with reasonable sample sizes. Sometimes it is more difficult to obtain acceptance of randomisation in rehabilitation patients than in acute patients. Some rehabilitation hospitals have only recently begun to take an interest in controlled clinical trials, hence are not so experienced. Nevertheless, controlled clinical trials delivering convincing results are possible in rehabilitation medicine as well. But biometrical consultation is necessary e.g. for study design, study conduction and evaluation. Most important points are the methodology of the study design and its practicability. Especially in these topics rehabilitation physicians and biometrician have to cooperate.

[Cost analysis of the treatment of patients with multiple trauma]

Current clinical management after multiple trauma is expensive. The aim of the present study was to quantify the actual costs of inpatient treatment after multiple trauma in a German university hospital, to compare the actual costs with the reimbursement rates, and to identify important determinants of costs. Routine documentation of hospital costs at a patient level was not available. Therefore a method for calculating the costs of resource utilization during clinical treatment of patients was developed. The concept was based on financial and utilization data provided by the hospital administration and patient-specific data. The average costs per case in the study group (mean ISS = 37) were 73.613 DM, maximal costs were up to 292.490 DM. The most costly components were intensive care, accounting for 60%, followed by procedures in the operating room (24%). A comparison with the reimbursement rates resulted in an average loss of 23.211 DM per case. Factors significantly associated with the costs of acute care hospitalization were outcome, injury severity, pattern of injury, blood volume replacement, length of mechanical ventilation, and number of operations. Whereas patient age, CNS state, mechanism of injury, pre-hospital care, and time between accident and hospital admission revealed no effect. Given the current reimbursement rates, multiple trauma care clearly belongs to those categories of care which have to be subsidized within the hospital. Any challenge to the optimal level of care resulting from this should be avoided.

[Prostanoid release and lipid peroxidation in patients with thoracic trauma]

There is compelling data from recent clinical studies on the impact of damage to the lung on the fate of traumatized patients. The lung reacts with a tremendous release of inflammatory mediators, but, on the other hand, this organ's ability in inactivating those factors is simultaneously attenuated. What is more, it is well known, that there often are no clinical signs of pulmonary dysfunction despite severe lung injury in the early posttraumatic phase. Therefore, in this prospective clinical study the following questions were addressed: (i) Is there any difference of the patients' lung response whether or not the (poly)trauma is associated with damage to the chest, (ii) either in the early or the late posttraumatic phase, and (iii) is there any marker that may prove to be a (significant) predictor of poor overall outcome?

METHODS

Upon approval of the local IRB/EC, 35 patients (pts) were enrolled who suffered from multiple injuries. The first blood samples were drawn at admission, then every two hours and in daily intervals. The plasma concentrations of following mediators were analyzed: prostanoids (PGI2, TxA2, PGE2, PGF2 alpha) and products of O2-radicals (malondialdehyde, conjugated dienes). All values were calculated on the basis of the actual plasma protein content to eliminate fluid-induced dilution effects. Subsets of pts were performed according to the different injury pattern: (i) pre-dominantly thoracic trauma (TX, n = 9); (ii) polytrauma with (PTX, n = 19), and (iii) without (PT, n = 7) damage to the lung.

RESULTS

As early as at admission, all pts revealed a severity-independent increase (p < 0.01) in most mediators' plasma levels. The pattern-related inflammatory response was most pronounced in casualties who had experienced thoracic trauma irrespective of whether it was combined with polytrauma. Within 1 to 3 days, the plasma levels of most mediators but PGE2 and MDA (all pts) as well as PGF2 alpha (PTX-group) normalized. The reactions of the lipid peroxidation products admitted of no group-differences.

CONCLUSIONS

Although there was a pattern-related release of (most) prostanoids which was rather pronounced in polytrauma associated with damage to the lung, we failed in proving any predictive marker to specifically estimate outcome, so far.

[Ulm Scientific Rehabilitation Research Group--"building blocks in rehabilitation"]

The Rehabilitation Research Network of Ulm on "Bausteine der Reha" consists of several departments of the University of Ulm, and various rehabilitation hospitals and cooperates with a pension insurance institute (LVA Wuerttemberg). The aim of this interdisciplinary approach is to evaluate process and outcome of rehabilitation measures considering specific clinical and rehabilitative questions with main emphasis on epidemiological and economic aspects. The Rehabilitation Research Nétwork of Ulm is subdivided into clinical projects and cross-sectional subjects. The clinical studies deal with cardiovascular and neurological rehabilitation and rehabilitation in disorders of the musculoskeletal system. The cross-sectional topics contain special fields such as biometry, health economics, epidemiology and occupational rehabilitation. All participating institutions have access to a central database with uniform structure of the data.

Early posttraumatic increase in production of nitric oxide in humans

Since nitric oxide (NO) contributes to both circulatory disorders and host defense, we analyzed the NO production in (poly)trauma patients (pts) in a prospective (pre)clinical study starting as early as at the scene of accident. Upon approval of the local IRB/EC, 85 multiple injured pts were enrolled. Subsets were performed according to trauma severity (ISS) and injury pattern, and between survivors versus nonsurvivors. The first blood sample was collected at the scene of accident, then in hourly to daily intervals. NO production was assessed by measuring nitrate+nitrite plasma levels. To estimate dilution effects, all values were calculated according to the actual plasma protein content. The extent of trauma was appraised by C-reactive protein (CRP) levels. Immediately after trauma, NO2-+NO3- plasma levels were always elevated. This was most pronounced in thoracic injury, irrespective of whether it was combined with multiple trauma. Nitrate+nitrite levels returned to normal within 24 h. CRP generation increased during 12 h following trauma and was most marked in severest trauma (ISS >50). For the first time, we show very early data following major trauma that demonstrate that NO overproduction starts immediately after trauma. However, systemic NO2-+NO3- levels actually reflect the severity of injury only during the first 2 h. Thereafter, NO generation is rather related to the individual trauma pattern, e.g., chest trauma. Nonetheless, the role of NO after severe trauma and especially in thoracic injury remains unclear and should further be elucidated in a specific study.

[Liberation of soluble CD14 (sCD 14) in plasma of trauma patients]

Membrane-fixed CD14 acts as a receptor for the protein-bound endotoxin (LPS) complex and mediates the cellular effects of endotoxin. Soluble CD14 (sCD14) is suggested to neutralize circulating LPS, i.e., acting as an endotoxin antagonist. The aim of this study was to elucidate the release of both sCD14 and endotoxin in traumatized patients, starting from the earliest phase after trauma. A total of 15 patients (O ISS = 19, 9-75) suffering major trauma were enrolled in this prospective study. Blood samples were collected as early as immediately at the site of accident, on hospital admission, and thereafter hourly, then daily. For patients (O ISS = 47) died within 24 h because of their severe injuries. Immediately after the accident as well as during the first 2 h after hospital admission, the mean sCD14 levels of surviving patients did not differ from those of healthy volunteers (n = 53). Thereafter, however, sCD14 increased continuously in the trauma group. The concentrations remained elevated throughout the entire observation period. There was, however, no relation between the sCD14 release and the pattern or the severity of injury. In contrast, endotoxin levels revealed a pattern-specific release. The highest plasma concentrations of LPS were observed in patients suffering from (additional) thoracic injury. On the basis of these results we conclude that the release of sCD14 after trauma does not reflect a strict principle such as action/reaction caused by the appearance of endotoxin immediately after the injury. Soluble CD14 is more likely release by an endotoxin-independent mechanism.

Is the activity of soluble CD14 enhanced following major trauma?

BACKGROUND

The molecule CD14 acts as a receptor for the protein-bound endotoxin (lipopolysaccharide [LPS]) complex and mediates the cellular effects of LPS. The soluble formation, sCD14, is supposed to neutralize circulating LPS (i.e., LPS antagonist) or transfer LPS effects to endothelial cells (i.e., LPS agonist).

OBJECTIVE

To elucidate the release of sCD14 per se in patients with major trauma in the early posttrauma period. Our a priori hypothesis was that sCD14 release depends on the plasma LPS concentration simultaneously measured.

PATIENTS

In a prospective study, 65 patients with multiple injuries (Injury Severity Score, 9-75) were enrolled. The patients were rescued by the medical helicopter service and directly admitted to our clinics. The plasma concentrations of sCD14 (enzyme immunoassay) and LPS (chromogenic limulus amebocyte lysate test) were analyzed. The first blood sample was collected immediately at the accident site. The following samples were drawn at intervals from 2 hours to daily for 2 weeks.

RESULTS

Sixty-one patients survived the observation time. Immediately after trauma, their mean sCD14 level was not different from that of healthy individuals. Two hours later, a pronounced increase of sCD14 was observed and sustained throughout the observation period. Even nonsurvivors showed an increased sCD14 release, but less pronounced. In all patients, plasma LPS levels were elevated during the first 12 hours.

CONCLUSIONS

Major trauma caused an increased release of sCD14. This elevation, however, was not correlated to LPS levels or to the severity of trauma (estimated by trauma scores). We found no evidence that sCD14 levels are of prognostic value regarding survival. Furthermore, the release of sCD14 did not occur in an LPS-neutralizing manner, but rendered possible an LPS-independent mechanism.

[Are ISS and PTS unsuitable trauma scores for prediction of (possible) post-traumatic lung failure?]

Prostanoids are inflammatory mediators which originate from endothelial cells following local tissue damage. That is why plasma levels of prostanoids are possible markers of inflammatory response and severity of trauma. We were able to demonstrate that the systemic release of prostanoids does not depend on the score values (ISS, PTS) but rather on different trauma patterns (chest trauma, head injury). Influencing vascular permeability and resistance elevated plasma levels of prostanoids may explain the impairment of pulmonary function in traumatized patients. It seems to be useful to re-evaluate the scoring systems with respect to chest trauma and head injury.

Identification of intracardiac thrombi in stroke patients with indium-111 platelet scintigraphy

Platelet scintigraphy (PSC) with indium-111 labelled platelets has been confirmed as an adequate method for the detection of intracardiac thrombi in patients with heart disease. We performed PSC of the heart and the neck vessels in 27 stroke patients with suspected cardiac embolism and as control on 10 patients with atherosclerotic lesions of the carotid arteries without evidence of heart disease. The carotid PSC was positive in 6 of 10 patients with carotid disease, and twice in the 27 with suspected cardiac embolism. In these 27 the PSC of the heart indicated pathological conditions 13 times. Pathological platelet accumulations could be visualized in 3 cases in the atrial space, in 9 cases in the region of the left ventricle, and once at the aortic valve. Scintigraphy was negative in all 10 patients with atherosclerosis of the neck vessels. The two-dimensional echocardiography revealed pathological findings in 8 of the 13 patients with positive heart PSC (3 with intraventricular thrombi, 3 with valvular disease, 2 with decreased ventricular contractility) and was normal in the 10 control patients. Open-heart surgery was performed in 2 patients with pathological PSC and revealed an intracardiac thrombus. Three of 4 patients with positive atrial PSC showed mitral or aortic valve disease. These results suggest that PSC can provide a valuable method for detecting cardiac thrombi in stroke patients.

Dual isotope carotid scintigraphy in patients with amaurosis fugax attacks

A new dual isotope scintigraphic (DISC) examination of the carotid arteries consisting of simultaneous injections of 111In-labeled platelets and 99mTc-labeled red cells was performed on eight male patients suffering from amaurosis fugax attacks. In concordance with the angiographically proven high percentage of significant extracranial carotid disease in patients with amaurosis fugax, six of the eight patients examined had an increased platelet accumulation in the carotid artery clinically affected. In one patient with normal angiography and one amaurosis fugax attack the platelet scintigraphy even revealed a pathological platelet accumulation in the ipsilateral carotid artery. These findings confirm the hypothesis that most amaurosis fugax attacks are due to arterio-arterial emboli originating from atherosclerotic plaques of the carotid bifurcation.