scholarly journals Bacteria-induced mineral precipitation: a mechanistic review

Microbiology ◽  
2021 ◽  
Vol 167 (4) ◽  
Author(s):  
Timothy D. Hoffmann ◽  
Bianca J. Reeksting ◽  
Susanne Gebhard
Keyword(s):  
Rational Design ◽  
Self Healing ◽  
Soil Consolidation ◽  
Mineral Precipitation ◽  
Redox States ◽  
Heavy Metal Remediation ◽  
Metal Redox ◽  
Micro Organisms ◽  
Application Specific ◽  
By Products

Micro-organisms contribute to Earth’s mineral deposits through a process known as bacteria-induced mineral precipitation (BIMP). It is a complex phenomenon that can occur as a result of a variety of physiological activities that influence the supersaturation state and nucleation catalysis of mineral precipitation in the environment. There is a good understanding of BIMP induced by bacterial metabolism through the control of metal redox states and enzyme-mediated reactions such as ureolysis. However, other forms of BIMP often cannot be attributed to a single pathway but rather appear to be a passive result of bacterial activity, where minerals form as a result of metabolic by-products and surface interactions within the surrounding environment. BIMP from such processes has formed the basis of many new innovative biotechnologies, such as soil consolidation, heavy metal remediation, restoration of historic buildings and even self-healing concrete. However, these applications to date have primarily incorporated BIMP-capable bacteria sampled from the environment, while detailed investigations of the underpinning mechanisms have been lagging behind. This review covers our current mechanistic understanding of bacterial activities that indirectly influence BIMP and highlights the complexity and connectivity between the different cellular and metabolic processes involved. Ultimately, detailed insights will facilitate the rational design of application-specific BIMP technologies and deepen our understanding of how bacteria are shaping our world.

scholarly journals A cookbook for DNase Hi-C

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Maria Gridina ◽  
Evgeniy Mozheiko ◽  
Emil Valeev ◽  
Ludmila P. Nazarenko ◽  
Maria E. Lopatkina ◽  
...  
Keyword(s):  
Rational Design ◽  
Restriction Enzymes ◽  
Nucleotide Exchange ◽  
Computational Tools ◽  
3 Dimensional ◽  
Cultured Human Cells ◽  
Dna Ends ◽  
By Products ◽  
Robust Protocol

Abstract Background The Hi-C technique is widely employed to study the 3-dimensional chromatin architecture and to assemble genomes. The conventional in situ Hi-C protocol employs restriction enzymes to digest chromatin, which results in nonuniform genomic coverage. Using sequence-agnostic restriction enzymes, such as DNAse I, could help to overcome this limitation. Results In this study, we compare different DNAse Hi-C protocols and identify the critical steps that significantly affect the efficiency of the protocol. In particular, we show that the SDS quenching strategy strongly affects subsequent chromatin digestion. The presence of biotinylated oligonucleotide adapters may lead to ligase reaction by-products, which can be avoided by rational design of the adapter sequences. Moreover, the use of nucleotide-exchange enzymes for biotin fill-in enables simultaneous labelling and repair of DNA ends, similar to the conventional Hi-C protocol. These improvements simplify the protocol, making it less expensive and time-consuming. Conclusions We propose a new robust protocol for the preparation of DNAse Hi-C libraries from cultured human cells and blood samples supplemented with experimental controls and computational tools for the evaluation of library quality.

scholarly journals Hydration-induced structural transitions in biomimetic tandem repeat proteins

2021 ◽  
Author(s):  
Romeo C. A. Dubini ◽  
Huihun Jung ◽  
Melik C. Demirel ◽  
Petra Rovó
Keyword(s):  
Tandem Repeat ◽  
High Performance ◽  
Rational Design ◽  
Dynamic Properties ◽  
Soft Segment ◽  
High Strength ◽  
Structural Rearrangement ◽  
Biological Materials ◽  
Self Healing ◽  
Structure Property

AbstractA major challenge in developing biomimetic, high-performance, and sustainable products is the accurate replication of the biological materials’ striking properties, such as high strength, self-repair, and stimuli-responsiveness. The rationalization of such features on the microscopic scale, together with the rational design of synthetic materials, is currently hindered by our limited understanding of the sequence-structure-property relationship. Here, employing state-of-the-art nuclear magnetic resonance (NMR) spectroscopy, we link the atomistic structural and dynamic properties of an artificial bioinspired tandem repeat protein TR(1,11) to its stunning macroscopic properties including high elasticity, self-healing capabilities, and recordholding proton conductivity amongst biological materials. We show that the hydration-induced structural rearrangement of the amorphous Gly-rich soft segment and the ordered Ala-rich hard segment is the key to the material’s outstanding physical properties. We found that in the hydrated state both the Ala-rich ordered and Gly-rich disordered parts contribute to the formation of the nanoconfined β-sheets, thereby enhancing the strength and toughness of the material. This restructuring is accompanied by fast proline ring puckering and backbone cis-trans isomerization at the water-protein interface, which in turn enhances the elasticity and the thermal conductivity of the hydrated films. Our in-depth characterization provides a solid ground for the development of next-generation materials with improved properties.

scholarly journals Disinfection by-products and extractable organic compounds in South African tap water

2008 ◽  
Vol 4 (1) ◽  
Author(s):  
Carien Nothnagel ◽  
Karsten Kotte ◽  
J J Pienaar ◽  
P G Van Zyl ◽  
J P Beukes
Keyword(s):  
Drinking Water ◽  
South African ◽  
Tap Water ◽  
Target Range ◽  
Preliminary Results ◽  
The Us ◽  
Microbiological Parameters ◽  
Us Epa ◽  
Micro Organisms ◽  
By Products

An important step in urban purification of drinking water is disinfection by e.g. chlorination where potential pathogenic micro-organisms in the water supply are killed. The presence of organic material in natural water leads to the formation of organic by- products during disinfection. Over 500 of these disinfection by-products (DBPs) have been identified and many more are estimated to form during the disinfection step. Several DBPs such as trihalomethanes (THMs), which is carcinogenic, poses serious health risks to the community. There is very few quantitative data available which realizes the actual levels of these compounds present in drinking water. The levels of four THMs present in drinking water were measured. It included chloroform, bromodichloromethane, chlorodibromomethane and bromoform. Although microbiological parameters are considered to get more attention than disinfection by-products, the measurement of the levels of these compounds in South-African drinking water is essential together with establishing minimum acceptable concentration levels. The target range for total trihalomethanes (TTHMs) established by the US EPA at the end of 2003 is 0-0.08ug/mL. The aim of this paper is to create an awareness of the problem as well as presenting preliminary results obtained with the method of analysis. Preliminary results indicate that urgent attention must be given to the regulation and monitoring of DBPs in South African drinking water.

Ozonation by-products issued from the destruction of microorganisms present in wastewaters treated for reuse

2004 ◽  
Vol 50 (2) ◽  
pp. 187-193 ◽  
Author(s):  
M.N. Rojas-Valencia ◽  
M.T. Orta-de-Velásquez ◽  
M. Vaca-Mier ◽  
V. Franco
Keyword(s):  
Amino Acids ◽  
Ascaris Suum ◽  
Correlation Coefficients ◽  
Salmonella Typhi ◽  
Faecal Coliforms ◽  
Excellent Correlation ◽  
Low Concentrations ◽  
Micro Organisms ◽  
By Products ◽  
Cellular Lysis

This work demonstrates the reaction of ozone on the amino acids comprising the covering layer of resistant micro-organisms. A secondary aim was to check the byproducts generated when ozone was applied to synthetic samples (such as Vibrio cholerae NO 01 WFCC-449, Salmonella typhi ATTC-6539, faecal coliforms and Ascaris suum). The ozone was applied at a concentration of 18.4 mgO3/min at pH 3, for different lengths of time. In the case of bacteria, results showed that, at 8 minutes, the number was reduced to the level of the Official Mexican Standards set for treated water destined for irrigation purposes (1,000 MPN/100 mL). Excellent correlation coefficients (0.95 to 0.99) were obtained for microbial concentrations versus ozone contact time. Destruction times required for 100% removal of the initial bacteria population varied between 2 and 14 minutes, while Ascaris suum required 1 hour. When Gram-negative bacteria die due to the effects of ozone, cellular lysis and the liberation of endotoxins (biodegradable) were observed. The ozonation of amino acids in the shell of Ascaris suum eggs, leads to the formation of aldehydes, such as formaldehyde and acetaldehyde, in low concentrations (0.0003 and 0.0005 μg/mL respectively). These levels are not hazardous to human health.

scholarly journals Rational Design of Stable Four-Electron-Accepting Carbonyl-N-methylpyridinium Species for High-Performance Lithium-Ion Batteries

2021 ◽  
Author(s):  
Xiaoming He ◽  
Xiujuan Wang ◽  
Wenhao Xue ◽  
Guangyuan Gao ◽  
Ling Chen ◽  
...  
Keyword(s):  
Lithium Ion Batteries ◽  
High Performance ◽  
Rational Design ◽  
Electrode Materials ◽  
Structural Evolution ◽  
Lithium Ion ◽  
Redox States ◽  
Redox Active ◽  
Organic Electrode ◽  
Organic Batteries

Development of novel organics that exhibit multiple and stable redox states, limited solubility and improved conductivity is a highly rewarding direction for improving the performance of lithium-ion batteries (LIBs). As biologically derived organic molecules, carbonylpyridinium compounds have desirable and tunable redox properties, making them suitable candidates for battery applications. In this work, we report a structural evolution of carbonylpyridinium-based redox-active organics, from 2-electron accepting BMP to 4-electron accepting small, conjugated molecules (1, 2), and then to the corresponding conjugated polymers (CP1, CP2). Through suppression of dissolution and increasing electrochemical conductivity, the LIBs performance can be gradually enhanced. At a relatively high current of 0.5 A g-1, high specific capacities for 1 (100 mAh g-1), 2 (260 mAh g-1), CP1 (360 mAh g-1) and CP2 (540 mAh g-1) can be reached after 240 cycles. Particularly, the rate performance and cycling stability of CP2 surpasses many reported commercial inorganic and organic electrode materials. This work provides a promising new carbonylpyridinium-based building block featured with multiple redox centers, on the way to high performance Li-organic batteries.

Self-Healing Concrete

2021 ◽  
Author(s):  
David Fisher
Keyword(s):  
Calcium Carbonate ◽  
Sulfate Reduction ◽  
Epoxy Resins ◽  
Cementitious Composites ◽  
Self Healing ◽  
Carbonate Formation ◽  
Micro Organisms

Self-healing techniques are most successful in preventing concrete from cracking or breaking. The book reviews the most promising methods, including the use of polymers, epoxy resins, fungi or cementitious composites; biomineralization, continuing hydration or carbonation or wet/dry cycling. Various micro-organisms are able to produce favorable effects, such as denitrification, calcium carbonate formation, sulfate reduction or the production of methane. The book references 289 original resources and includes their direct web link for in-depth reading.

scholarly journals In-Depth Profiling of Calcite Precipitation by Environmental Bacteria Reveals Fundamental Mechanistic Differences with Relevance to Application

2020 ◽  
Vol 86 (7) ◽  
Author(s):  
Bianca J. Reeksting ◽  
Timothy D. Hoffmann ◽  
Linzhen Tan ◽  
Kevin Paine ◽  
Susanne Gebhard
Keyword(s):  
Calcium Carbonate ◽  
Rational Design ◽  
Urease Activity ◽  
Depth Profiling ◽  
Growth Conditions ◽  
Self Healing ◽  
Calcite Precipitation ◽  
Geological Features ◽  
Inorganic Composition ◽  
Environmental Bacteria

ABSTRACT Microbially induced calcite precipitation (MICP) has not only helped to shape our planet’s geological features but is also a promising technology to address environmental concerns in civil engineering applications. However, limited understanding of the biomineralization capacity of environmental bacteria impedes application. We therefore surveyed the environment for different mechanisms of precipitation across bacteria. The most fundamental difference was in ureolytic ability, where urease-positive bacteria caused rapid, widespread increases in pH, whereas nonureolytic strains produced such changes slowly and locally. These pH shifts correlated well with patterns of precipitation on solid medium. Strikingly, while both mechanisms led to high levels of precipitation, we observed clear differences in the precipitate. Ureolytic bacteria produced homogenous, inorganic fine crystals, whereas the crystals of nonureolytic strains were larger and had a mixed organic/inorganic composition. When representative strains were tested in application for crack healing in cement mortars, nonureolytic bacteria gave robust results, while ureolytic strains showed more variation. This may be explained by our observation that urease activity differed between growth conditions or by the different natures and therefore different material performances of the precipitates. Our results shed light on the breadth of biomineralization activity among environmental bacteria, an important step toward the rational design of bacterially based engineering solutions. IMPORTANCE Biomineralization triggered by bacteria is important in the natural environment and has many applications in industry and in civil and geotechnical engineering. The diversity in biomineralization capabilities of environmental bacteria is, however, not well understood. This study surveyed environmental bacteria for their ability to precipitate calcium carbonate minerals and investigated both the mechanisms and the resulting crystals. We show that while urease activity leads to the fastest precipitation, it is by no means essential. Importantly, the same quantities of calcium carbonate are produced by nonureolytic bacteria, and the resulting crystals appear to have larger volumes and more organic components, which are likely beneficial in specific applications. Testing both precipitation mechanisms in a self-healing concrete application showed that nonureolytic bacteria delivered more robust results. Here, we performed a systematic study of the fundamental differences in biomineralization between environmental bacteria, and we provide important information for the design of bacterially based engineering solutions.

Colonic acetate in obesity: location matters!

2016 ◽  
Vol 130 (22) ◽  
pp. 2083-2086 ◽  
Author(s):  
Laure B. Bindels ◽  
Isabelle Leclercq
Keyword(s):  
Fatty Acids ◽  
Animal Models ◽  
Short Chain Fatty Acids ◽  
Host Immunity ◽  
Short Chain ◽  
Therapeutic Application ◽  
Complex Interactions ◽  
Micro Organisms ◽  
By Products ◽  
Chain Fatty Acids

Gut micro-organisms are recognized as crucial regulators of host immunity and the microbiota has been implicated in several inflammatory, immune, inflammatory or even psychiatric disorders. Therefore the analysis of the complex interactions between gut microbiota and the host is currently under intense investigation. Most of our knowledge stems from the study of animal models while translational research and data in humans are necessary to move the field forward and to evolve to diagnostic and therapeutic application. Amongst the microbial by-products, short chain fatty acids such as acetate yielded by fermentation of non-digestible fibers, were pointed as metabolic modulators. Here we highlight a study evaluating the effects of colonic infusion of one of the short chain fatty acids, acetate, in a cohort of overweight and obese normoglycaemic subjects.

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