scholarly journals Construction of an inducible amyloid expression circuit in Bacillus megaterium: A case study with CsgA and TasA

2019 ◽  
Author(s):  
Elin M. Larsson ◽  
John B. McManus ◽  
Richard M. Murray
Keyword(s):  
Synthetic Biology ◽  
Cell Survival ◽  
Bacillus Megaterium ◽  
Biofilm Formation ◽  
Water Remediation ◽  
Hostile Environment ◽  
Promising Candidate ◽  
Functional Amyloids ◽  
Future Work

AbstractEnvironmental applications of synthetic biology such as water remediation require engineered strains to function robustly in a fluctuating and potentially hostile environment. The construction of synthetic biofilm formation circuits could potentially alleviate this issue by promoting cell survival. Towards this end, we construct a xylose-inducible system for the expression of the functional amyloids CsgA and TasA in the soil bacterium Bacillus megaterium. We find that although both amyloids are expressed, only TasA is successfully exported from the cells. Furthermore, expression of CsgA results in a significant growth penalty for the cells while expression of TasA does not. Finally, we show that TasA expression conveys a small but detectable increase in cells’ adhesion to nickel beads. These results suggest that TasA is a promising candidate for future work on synthetic biofilm formation in B. megaterium.

scholarly journals Biosurfactant production by a Bacillus megaterium strain

2020 ◽  
Vol 15 (1) ◽  
pp. 629-637
Author(s):  
Mihaela Marilena Stancu
Keyword(s):  
Yeast Extract ◽  
Bacillus Megaterium ◽  
Biofilm Formation ◽  
Petroleum Hydrocarbon ◽  
Biosurfactant Production ◽  
Positive Bacterium ◽  
Promising Candidate ◽  
Ph Values ◽  
Proteose Peptone ◽  
Long Chain

AbstractThe aim of the present study was to investigate the ability of Bacillus megaterium IBBPo17 (GenBank KX499518) cells to produce biosurfactant when the growth was done in the presence of long-chain n-alkane n-hexadecane on medium supplemented with yeast extract, proteose peptone, starch, or cellulose. B. megaterium IBBPo17 revealed a higher growth in the presence of n-hexadecane when the medium was supplemented with yeast extract, proteose peptone, or starch, compared with cellulose. Biosurfactant production was higher when B. megaterium IBBPo17 was grown in the presence of n-hexadecane on yeast extract, proteose peptone, or starch supplemented medium, compared with biosurfactant produced on cellulose supplemented medium. A direct correlation between cell growth and biosurfactant production was observed. When the growth of B. megaterium IBBPo17 cells was higher, the decrease in pH values of the medium was higher too, and more amount of CO2 was released. Changes in cell morphology, aggregation of the cells in clusters, and biofilm formation were observed when B. megaterium IBBPo17 was grown in the presence of n-hexadecane on medium supplemented with yeast extract, proteose peptone, starch, or cellulose. Due to its physiological abilities, this Gram-positive bacterium could be a promising candidate for the bioremediation of petroleum hydrocarbon polluted environments.

scholarly journals Anti-Biofilm Molecules Targeting Functional Amyloids

Antibiotics ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 795
Author(s):  
Leticia Matilla-Cuenca ◽  
Alejandro Toledo-Arana ◽  
Jaione Valle
Keyword(s):  
Biofilm Formation ◽  
Therapeutic Strategy ◽  
Research Area ◽  
Therapeutic Strategies ◽  
Structural Components ◽  
Significant Issue ◽  
Wide Range ◽  
Effective Therapeutic Strategy ◽  
Functional Amyloids ◽  
Biofilm Matrix

The choice of an effective therapeutic strategy in the treatment of biofilm-related infections is a significant issue. Amyloids, which have been historically related to human diseases, are now considered to be prevailing structural components of the biofilm matrix in a wide range of bacteria. This assumption creates the potential for an exciting research area, in which functional amyloids are considered to be attractive targets for drug development to dissemble biofilm structures. The present review describes the best-characterized bacterial functional amyloids and focuses on anti-biofilm agents that target intrinsic and facultative amyloids. This study provides a better understanding of the different modes of actions of the anti-amyloid molecules to inhibit biofilm formation. This information can be further exploited to improve the therapeutic strategies to combat biofilm-related infections.

scholarly journals The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Dagmar Waltemath ◽  
Martin Golebiewski ◽  
Michael L Blinov ◽  
Padraig Gleeson ◽  
Henning Hermjakob ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Data Model ◽  
Computational Models ◽  
Life Sciences ◽  
The Past ◽  
Challenges And Opportunities ◽  
Stakeholder Workshop ◽  
Software Engineers ◽  
Future Work ◽  
Modeling In Biology

AbstractThis paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

scholarly journals Extending Multilevel Statistical Entropy Analysis towards Plastic Recyclability Prediction

2021 ◽  
Vol 13 (6) ◽  
pp. 3553
Author(s):  
Philippe Nimmegeers ◽  
Alexej Parchomenko ◽  
Paul De Meulenaere ◽  
Dagmar R. D’hooge ◽  
Paul H. M. Van Steenberge ◽  
...  
Keyword(s):  
Circular Economy ◽  
Real Life ◽  
Plastic Waste ◽  
Entropy Analysis ◽  
Waste Collection ◽  
Statistical Entropy ◽  
Waste Streams ◽  
Material Component ◽  
Future Work

Multilevel statistical entropy analysis (SEA) is a method that has been recently proposed to evaluate circular economy strategies on the material, component and product levels to identify critical stages of resource and functionality losses. However, the comparison of technological alternatives may be difficult, and equal entropies do not necessarily correspond with equal recyclability. A coupling with energy consumption aspects is strongly recommended but largely lacking. The aim of this paper is to improve the multilevel SEA method to reliably assess the recyclability of plastics. Therefore, the multilevel SEA method is first applied to a conceptual case study of a fictitious bag filled with plastics, and the possibilities and limitations of the method are highlighted. Subsequently, it is proposed to extend the method with the computation of the relative decomposition energies of components and products. Finally, two recyclability metrics are proposed. A plastic waste collection bag filled with plastic bottles is used as a case study to illustrate the potential of the developed extended multilevel SEA method. The proposed extension allows us to estimate the recyclability of plastics. In future work, this method will be refined and other potential extensions will be studied together with applications to real-life plastic products and plastic waste streams.

scholarly journals Vesicle-associatedPseudomonas aeruginosaleucine aminopeptidase modulates bacterial biofilms grown on host cellular substrates

2019 ◽  
Author(s):  
Caitlin N. Esoda ◽  
Meta J. Kuehn
Keyword(s):  
Biofilm Formation ◽  
Chronic Wounds ◽  
Membrane Vesicles ◽  
Outer Membrane Vesicles ◽  
Bacterial Biofilm ◽  
Lung Epithelial ◽  
Coculture Model ◽  
Chronic Colonization ◽  
Bacterial Outer Membrane ◽  
Future Work

AbstractPseudomonas aeruginosa, known as one of the leading causes of morbidity and mortality in cystic fibrosis (CF) patients, secretes a variety of virulence-associated proteases. These enzymes have been shown to contribute significantly toP. aeruginosapathogenesis and biofilm formation in the chronic colonization of CF patient lungs, as well as playing a role in infections of the cornea, burn wounds and chronic wounds. Our lab has previously characterized a secretedP. aeruginosapeptidase, PaAP, that is highly expressed in chronic CF isolates. This leucine aminopeptidase is not only secreted solubly, it also associates with bacterial outer membrane vesicles (OMVs), structures known for their contribution to virulence mechanisms in a variety of Gram-negative species and one of the major components of the biofilm matrix. With this in mind, we hypothesized that PaAP may play a role inP. aeruginosabiofilm formation. Using a lung epithelial cell/bacterial biofilm coculture model, we show that PaAP deletion in a clinicalP. aeruginosabackground leads to increased early biofilm formation. We additionally found that only native vesicle-bound PaAP, as opposed to its soluble forms, could reconstitute the original PaAP-mediated inhibition phenotype, and that the PaAP-containing vesicles could disperse preformed biofilm microcolonies ofKlebsiella pneumoniae, another lung pathogen. These data provide the basis for future work into the mechanism behind PaAP-OMV mediated bacterial microcolony dispersal and the application of these findings to clinical anti-biofilm research.

scholarly journals Chaperones mainly suppress primary nucleation during formation of functional amyloid required for bacterial biofilm formation

2022 ◽  
Author(s):  
Madhu Nagaraj ◽  
Zahra Najarzadeh ◽  
Jonathan Pansieri ◽  
Ludmilla A. Morozova-Roche ◽  
Henrik Biverstål ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Biofilm Formation ◽  
Bacterial Biofilm ◽  
Functional Amyloid ◽  
E Coli ◽  
Primary Nucleation ◽  
Functional Amyloids

Unlike misfolding in neurodegenerative diseases, aggregation of functional amyloids involved in bacterial biofilm, e.g. CsgA (E. coli) and FapC (Pseudomonas), is carefully regulated. However, it is unclear whether functional aggregation...

scholarly journals Analysing Ship Nox Emissions with Hadoop A Case Study for the Port of Rotterdam

2017 ◽  
Vol 3 (3) ◽  
pp. 14 ◽  
Author(s):  
Frank Cremer ◽  
Muktha Muralee
Keyword(s):  
Geographical Area ◽  
Big Data Analytics ◽  
Sustainable Growth ◽  
Strategic Decision ◽  
Geographical Information ◽  
Atmospheric Emissions ◽  
Deposition Model ◽  
Position Data ◽  
Future Work

Atmospheric emissions such as NOx from ship engines have a drastic impact on the environment. Controlling them is crucial for maintaining a sustainable growth for any logistics company. The Port of Rotterdam (The Netherlands) is using big data analytics to gain actionable insights into these emissions. Our case study deals with the implementation of the emission calculations and reporting implemented in Hadoop. In the analytical setup we introduce the method for estimating emissions based on recorded ship position data and information about its engines. We present a flexible approach that stores intermediate results allowing different levels of aggregation. These levels of aggregations are per geographical area, per grid or for a whole journey attributed to each visited berth. The results are visualized in a Geographical Information System (GIS). The estimated atmospheric emissions also serves as input for the deposition model. We present some selected results of emissions per grid as well as for pre-defined areas. These results are used by the port to make strategic decision. For future work we recommend to also implement the deposition model in Hadoop as this model is also calculative intensive and therefore it currently only accepts aggregated emissions as input, whereby its accuracy is most likely reduced.

scholarly journals MindTick: Case Study of a Digital System for Mental Health Clinicians to Monitor and Support Patients Outside Clinics

2021 ◽  
Author(s):  
Rebecca Perry ◽  
Lydia Oakey-Neate ◽  
John Fouyaxis ◽  
Sue Boyd-Brierley ◽  
Megan Wilkinson ◽  
...  
Keyword(s):  
Mental Health ◽  
Healthcare Service ◽  
Mobile App ◽  
Health Conditions ◽  
Mental Health Clinicians ◽  
Psychological Service ◽  
Mental Health Patients ◽  
Future Work ◽  
Roll Out

The current COVID-19 pandemic has highlighted the limitations of relying solely on in-person contact for diagnosis, monitoring and treatment of mental health conditions. Mobile health approaches can be used to monitor mental health patients remotely, but they are not properly integrated with existing models of healthcare service delivery. We present findings from a case study of a mobile app enabled cloud-based software program rolled out in a phone based psychological service to enable real-time/temporal monitoring. The program offered patients an app to record measures of symptoms in everyday contexts and provided clinicians with access to an accompanying dashboard to use information from the app to tailor treatments and monitor progress and ultimately facilitate earlier and personalised care decisions. Feedback related to implementation and utility was gathered from clinicians through a focus group conducted two months post-roll-out. Findings identified that the system is valuable and feasible, however implementation issues were identified. These are discussed in order to inform future work in this area to support the delivery of timely and responsive mental health care in the community.

scholarly journals Identification of Paleoearthquakes and Coseismic Slips on a Normal Fault Using High-Precision Quantitative Morphology: Application to the Jiaocheng Fault in the Shanxi Rift, China

Lithosphere ◽  
2021 ◽  
Vol 2021 (Special 2) ◽  
Author(s):  
Junjie Zou ◽  
Honglin He ◽  
Yusuke Yokoyama ◽  
Adam D. Sproson ◽  
Yoshiki Shirahama ◽  
...  
Keyword(s):  
Active Faults ◽  
Normal Fault ◽  
Seismic Events ◽  
Quantitative Morphology ◽  
Coseismic Slip ◽  
Slip History ◽  
Absolute Dating ◽  
Future Work ◽  
Shanxi Rift

Abstract The quantitative morphology of bedrock fault surfaces combined with aerial surveys and field identification is a useful approach to identify paleoearthquakes, obtain coseismic slips, and evaluate the seismogenic capacity of active faults in bedrock areas where traditional trenching methods are not applicable. Here, we report a case study of the Jiaocheng Fault (JCF) in the Shanxi Rift, China. Although several studies have been conducted on the JCF, its coseismic slip history and seismogenic capacity are still unclear. To address these problems, we investigated two bedrock fault surfaces, Sixicun (SXC) and Shanglanzhen (SLZ), on the JCF’s northern segment using quantitative morphological analysis together with aerial and field surveys. Quantitative fractal analysis based on the isotropic empirical variogram and moving window shows that both bedrock fault surfaces have the characteristics of vertical segmentation, which is likely due to periodic earthquakes, the coseismic slip of which can be determined by the height of the segments. Three seismic events at SXC, with a coseismic vertical slip of 1.74, 1.65, and 1.99 m, and three seismic events at SLZ, with a coseismic vertical slip of 1.32, 2.35, and 1.88 m, are identified. Compared with the previous studies, these three seismic events may occur in the Holocene, but it requires absolute dating ages to support, which is also the focus of our future work. Considering the seismologic capability (M>7.5) and the relationship between the recurrence interval of ~2.6 kyr and elapsed time of more than 3 kyr, the seismic hazard of the northern and middle segments of the JCF requires immediate attention.

scholarly journals Environmental impacts on the design and arts environment for industry 3.0 cotton roller ginning process

2021 ◽  
Vol 8 (1) ◽  
pp. 22-34
Author(s):  
Vijayan Gurumurthy Iyer
Keyword(s):  
Impact Assessment ◽  
Environmental Impacts ◽  
Sustainable Design ◽  
Research Work ◽  
Water Remediation ◽  
Design Environment ◽  
Hazardous Waste Management ◽  
The Past ◽  
Disease Impact

The past five decades have been characterised by passage of the environmental impact assessment (EIA) legislation dealing with the environment, including legislation on the control of land, air and water pollution, solid and hazardous waste management, resource conservation and recovery, and soil and ground water and surface water remediation. The aim of this research is to investigate and discuss coronavirus and byssinosis disease impact assessment. Sustainable development is the artistic idea that science and humanities must live and meet their needs without compromising the efficacy and efficiency of future generations to meet their own needs. Prediction and assessment of environmental impacts (effects) on the design and arts environment for industry 3.0 cotton roller ginning process is provided. Sustainable design and arts are discussed in this research work. EIA of conventional design and arts is also investigated. Sustainable design and arts environment for cotton ginning process is presented. The case study and check of strengthening of agricultural extension through sustainable entrepreneurship is discussed in this article.   Keywords: Agriculture, arts, cotton, design, environment, entrepreneurship, ginning, sustainability.

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