Population dynamics of bacteria introduced into bentonite amended soil

Bacteria have frequently been introduced into the soil environment, e.g. for increasing crop production or for biological control purposes. Many applications require high numbers of surviving organisms in order to be effective. However, survival of bacteria after introduction into soil is generally poor, and numbers of introduced bacteria have been known to decrease from 10 9to approximately 10 3cells/g soil in 25 days. Thus, if bacteria are to be used as effective microbial inoculants to, a means to increase survival levels in soil needs to be found.Survival of Rhizobium leguminosarum biovar trifolii introduced into loamy sand was found to be greatly enhanced by amendments of bentonite, in amounts of 5 or 10%, to the soil. Bentonite appeared to offer introduced bacteria protection against protozoan predation, resulting in increased bacterial survival levels in bentonite amended soil as compared to unamended soil.Also in liquid cultures, protozoan activity was strongly hampered by the presence of bentonite, thereby also improving the survival of Rhizobium. Bentonite did not release any substances toxic to protozoa in liquid cultures, and presumably this would not occur in the soil environment either. Bentonite toxicity could therefore not explain the increased survival levels of bacteria introduced into bentonite amended soil. It was suggested that, in liquid cultures, bentonite clay increased the minimum level of bacteria for effective predation by protozoa.Changes in soil structure as a result of bentonite additions could explain the observed increases in bacterial survival levels. A mathematical relationship was found describing the log numbers of introduced rhizobia surviving in soil samples after an incubation period of 57 days using 3 pore size classes. Pores with necks < 3 μm and between 3 and 6 μm positively affected survival levels. These pores apparently were large enough to allow bacteria to enter, but were too small to be accessible to predating protozoa. Pores with necks between 6 and 15 μm had a negative influence on rhizobial survival levels, because bacteria situated inside these relatively large pores could be reached and predated upon by protozoa. Therefore, pores < 6 μm were found so serve as protective microhabitats for bacteria introduced into soil. A larger number of such protective microhabitats in bentonite amended loamy sand than in unamended loamy sand could explain the observed increase in survival levels of bacteria introduced into bentonite amended soil. The colonization potential of protective microhabitats was suggested to be determined largely by pore shape and the continuity of the water-filled pore system. Increased numbers of protective microhabitats (pores < 6 μm) in bentonite-amended soil as compared to unamended soil were demonstrated visually by micro-morphoiogical studies using Cryo Scanning Electron Microscopy.The effectiveness of bentonite was strongly determined by the way in which the clay and the inoculum were added to the soil. When a bentonite suspension and bacteria were mixed together prior to inoculation, the clay offered more protection against predation than when bentonite powder and bacteria were added separately. This suggested that when the protective agent was present at the site of introduction, a more efficient use of the clay could be made, resulting in enhanced survival levels.Apart from survival, bentonite additions to soil also influenced bacterial respiration. The cumulative amount of CO 2 respired by rhizobia introduced into sterile bentonite- amended loamy sand was significantly higher than in unamended loamy sand. Carbon was used more efficiently during growth in bentonite-amended than in unamended loamy sand. The maintenance respiration of rhizobial cells was not influenced by the presence of bentonite clay. The growth rate of rhizobia introduced into sterile soil was increased by the presence of bentonite.Pseudomonas fluorescens was also found to survive at higher levels in bentoniteamended than in unamended soil, suggesting the bentonite effects were not limited to Rhizobium only. Pseudomonas fluorescens was used to study root colonization by bacteria introduced into bentonite amended soil. A rhizosphere effect (i.e. the occurrence of higher cell concentrations in rhizosphere soil than in bulk soil) was observed both in the absence and in the presence of bentonite clay, but it was less pronounced in the latter case. This finding suggested that bacteria were physically hindered by bentonite, making it more difficult to invade the immediate root environment. However, protection against predation by bentonite enhanced survival to such an extent, that overall survival in the rhizosphere was still higher in bentonite amended loamy sand than in the unamended soil.It can be concluded from this thesis that soil structure, and especially the pore size distribution of the soil is a key factor determining the survival, chances of bacteria introduced into soil. Application of introduced bacteria for e.g. biological control will probably stand a larger chance of being successful in soils with relatively high numbers of pores < 6 μm However, it is unlikely that bentonite will ever be applied to soil in amounts of e.g. 5%, because of the large impact of bentonite additions on, for example, the moisture characteristics of the soil. However, the knowledge obtained on the importance of the pore size distribution of a soil, and the fact that the she of introduction of the bacteria will largely determine survival chances, will be of great importance for the future development of successful carrier materials for introducing bacteria into soil

Pandemic Influenza and Healthcare Demand in the Netherlands: Scenario Analysis

In accordance with World Health Organization guidelines, the Dutch Ministry of Health, Welfare and Sports designed a national plan to minimize effects of pandemic influenza. Within the scope of the Dutch pandemic preparedness plan, we were asked to estimate the magnitude of the problem in terms of the number of hospitalizations and deaths during an influenza pandemic. Using scenario analysis, we also examined the potential effects of intervention options. We describe and compare the scenarios developed to understand the potential impact of a pandemic (i.e., illness, hospitalizations, deaths), various interventions, and critical model parameters. Scenario analysis is a helpful tool for making policy decisions about the design and planning of outbreak control management on a national, regional, or local level

The prognostic value of vascular endothelial growth factor in 574 node-negative breast cancer patients who did not receive adjuvant systemic therapy

The growth and metastasising capacity of solid tumours are dependent on angiogenesis. Vascular endothelial growth factor is a mediator of angiogenesis. In this study we investigated whether vascular endothelial growth factor is associated with the natural course of the disease in primary invasive breast cancer. In 574 tumours of patients with node-negative invasive breast cancer the cytosolic levels of vascular endothelial growth factor were measured using a quantitative enzyme-linked immunosorbent assay. These patients did not receive adjuvant systemic therapy and were followed for a median follow-up time of 61 months (range 2–155 months) after the primary diagnosis. Correlations with well-known prognostic factors, and univariate and multivariate survival analyses were performed. Vascular endothelial growth factor level was positively associated with age and tumour size (P=0.042 and P=0.029, respectively). In addition, vascular endothelial growth factor level was inversely, but weakly correlated with progesterone receptor levels (PgR) (rs=−0.090, P=0.035). A high vascular endothelial growth factor level (equal or above the median level of 0.53 ng mg−1 protein) predicted a reduced relapse-free survival and overall survival in the univariate survival rate analysis (for both P=0.005). In the multivariate analysis as well, vascular endothelial growth factor showed to be an independent predictor of poor relapse-free survival and overall survival (P=0.045 and P=0.029, respectively), in addition to age, tumour size and PgR. The results show that cytosolic levels of vascular endothelial growth factor in tumour tissue samples are independently indicative of prognosis for patients with node-negative breast cancer who were not treated with adjuvant systemic therapy. This implies that vascular endothelial growth factor is related with the natural course of breast cancer progression

Was There Shortening of the Interval Between Diagnosis and Treatment of Colorectal Cancer in Southern Netherlands Between 2005 and 2008?

Background: The Dutch Cancer Society proposed that the interval between diagnosis and start of treatment should be less than 15 working days. The purpose of this study was to determine whether the interval from diagnosis to treatment for patients with colorectal cancer (CRC) shortened between 2005 and 2008 in hospitals in southern Netherlands. Methods: Patients with CRC diagnosed in six hospitals in southern Netherlands during January to December in 2005 (n = 445) and January to July in 2008 (n = 353) were included. The time between diagnosis and start of treatment was assessed, and the proportion of patients treated within the recommended time (70 years and those with stage I disease. Substantial variation was seen among hospitals. Conclusions: Time to treatment for patients with CRC in southern Netherlands did not shorten between 2005 and 2008. The time to treatment should be reduced to meet the advice of the Dutch Cancer Society

Diagnostic DNA Methylation Biomarkers for Renal Cell Carcinoma:A Systematic Review

CONTEXT: The 5-yr survival of early-stage renal cell carcinoma (RCC) is approximately 93%, but once metastasised, the 5-yr survival plummets to 12%, indicating that early RCC detection is crucial to improvement in survival. DNA methylation biomarkers have been suggested to be of potential diagnostic value; however, their current state of clinical translation is unclear and a comprehensive overview is lacking. OBJECTIVE: To systematically review and summarise all literature regarding diagnostic DNA methylation biomarkers for RCC. EVIDENCE ACQUISITION: We performed a systematic literature review of PubMed, EMBASE, Medline, and Google Scholar up to January 2019, according to the Preferred Reporting Items for Systematic Review and Meta-Analysis of Diagnostic Test Accuracy Studies (PRISMA-DTA) guidelines. Included studies were scored according to the Standards for Reporting of Diagnostic Accuracy Studies (STARD) criteria. Forest plots were generated to summarise diagnostic performance of all biomarkers. Level of evidence (LoE) and potential risk of bias were determined for all included studies. EVIDENCE SYNTHESIS: After selection, 19 articles reporting on 44 diagnostic DNA methylation biomarkers and 11 multimarker panels were included; however, only 15 biomarkers were independently validated. STARD scores varied from 4 to 13 out of 23 points, with a median of 10 points. Large variation in subgroups, methods, and primer locations was observed. None of the reported biomarkers exceeded LoE III, and the majority of studies reported inadequately. CONCLUSIONS: None of the reported biomarkers exceeded LoE III, indicating their limited clinical utility. Moreover, study reproducibility and further development of these RCC biomarkers are greatly hampered by inadequate reporting. PATIENT SUMMARY: In this report, we reviewed whether specific biomarkers could be used to diagnose the most common form of kidney cancer. We conclude that due to limited evidence and reporting inconsistencies, none of these biomarkers can be used in clinical practice, and further development towards clinical use is hindered

A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA)

Motivation: We address the following question: Does inhibition of the expression of a gene X in a cellular assay affect the expression of another gene Y? Rather than inhibiting gene X experimentally, we aim at answering this question computationally using as the only input observational gene expression data. Recently, a new statistical algorithm called Intervention calculus when the Directed acyclic graph is Absent (IDA), has been proposed for this problem. For several biological systems, IDA has been shown to outcompete regression-based methods with respect to the number of true positives versus the number of false positives for the top 5000 predicted effects. Further improvements in the performance of IDA have been realized by stability selection, a resampling method wrapped around IDA that enhances the discovery of true causal effects. Nevertheless, the rate of false positive and false negative predictions is still unsatisfactorily high. Results: We introduce a new resampling approach for causal discovery called accumulation IDA (aIDA). We show that aIDA improves the performance of causal discoveries compared to existing variants of IDA on both simulated and real yeast data. The higher reliability of top causal effect predictions achieved by aIDA promises to increase the rate of success of wet lab intervention experiments for functional studies

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches

Development of two patient self-reported measures on functional health Status (FOD) and Health-Related Quality of Life (QOD) in adults with oropharyngeal dysphagia using the Delphi technique

Introduction: Patient self-evaluation is an important aspect in the assessment of dysphagia and comprises both Functional Health Status (FHS) and Health-Related Quality of Life (HR-QoL). As many measures combine both FHS and HR-QoL, disease-related functioning cannot be distinguished from disease-related quality of life as experienced by the patient. Moreover, current patient self-reported measures are limited by poor and incomplete data on psychometric properties. Objective. This study aimed to establish content validity for the development of two new self-reported measures on FHS and HR-QoL in adults with oropharyngeal dysphagia (OD), in line with the psychometric taxonomy and guidelines from the COSMIN group (COnsensus-based Standards for the selection of health Measurement INstruments). Methods. Using the Delphi technique, international expert consensus was achieved; participants and patients with dysphagia evaluated relevance, comprehensiveness, and comprehensibility of definitions of relevant constructs (i.e., dysphagia, FHS and HR-QoL) and potential items. Results: A total of 66 Delphi participants from 45 countries achieved consensus across two rounds. The Delphi study resulted in two prototype measures, the Functional health status measure of Oropharyngeal Dysphagia (FOD) and the health-related Quality of life measure of Oropharyngeal Dysphagia (QOD), consisting of 37 and 25 items, respectively. Minimal revisions were required based on feedback by patients. Conclusions: This study provides evidence of good content validity for both newly developed prototype measures FOD and QOD. Future studies will continue the process of refining the measures, and evaluate the remaining psychometric properties using both Classic Test Theory (CTT) and Item Response Theory (IRT) models.Otorhinolaryngolog