Microbial ureases: significance, regulation, and molecular characterization

NiII and CoII binary and ternary complexes of 3-formylchromone: spectroscopic characterization, antimicrobial activities, docking and modeling studies

Reactions of 3-formylchromone (L) with Ni(ii) and Co(ii) ions having different anions (acetate, perchlorate, nitrate, and chloride) yielded a series of binary and ternary octahedral complexes with the general formula [ML n L' m X y (S) a ]Z y ·bS, where M = Ni or Co, n = 1-3, L' = auxiliary ligand = 8-hydroxyquinoline or 1,10-phenanthroline, m = 1 or 2, X = acetate or chloride, y = 0 or 2, S = H2O or MeOH, a = 0-2, Z = nitrate or perchlorate and b = 0-1.5. Elemental and thermal analyses and infra-red, electronic, mass, magnetic susceptibility and molar conductivity measurements were successfully utilized to characterize the structures of the chromone complexes. The chromone ligand acts as a neutral bidentate ligand through its formyl and γ-pyrone oxygen atoms. The obtained complexes were formed with molar ratios 1 : 2 and 1 : 3 M : L for the binary and 1 : 2 : 1 and 1 : 1 : 1 M : L : L' for the ternary complexes. The kinetic parameters of the thermal degradation steps were estimated and explained using the Coats-Redfern equations. The synthesized complexes showed antimicrobial activity with higher activity toward Candida albicans and Bacillus subtilis. Docking studies showed good agreement with the antimicrobial activity. Molecular modeling of the synthesized complexes was performed using Hyperchem at the PM3 level and the calculated structures correlate with the experimental data.

New Triazinoindole Bearing Benzimidazole/Benzoxazole Hybrids Analogs as Potent Inhibitors of Urease: Synthesis, In Vitro Analysis and Molecular Docking Studies

Twenty-four analogs based on triazinoindole bearing benzimidazole/benzoxazole moieties (1-25) were synthesized. Utilizing a variety of spectroscopic methods, including 1H-, 13C-NMR, and HREI-MS, the newly afforded compounds (1-25) were analyzed. The synthesized analogs were tested against urease enzyme (in vitro) as compared to the standard thiourea drug. All triazinoindole-based benzimidazole/benzoxazole analogs (1-25) exhibited moderate to excellent inhibition profiles, having IC50 values of 0.20 ± 0.01 to 36.20 ± 0.70 μM when evaluated under the positive control of thiourea as a standard drug. To better understand the structure-activity relationship, the synthesized compounds were split into two groups, "A" and "B." Among category "A" analogs, analogs 8 (bearing tri-hydroxy substitutions at the 2,4,6-position of aryl ring C) and 5 (bearing di-hydroxy substitutions at the 3,4-position of aryl ring C) emerged as the most potent inhibitors of urease enzyme and displayed many times more potency than a standard thiourea drug. Besides that, analog 22 (which holds di-hydroxy substitutions at the 2,3-position of the aryl ring) and analog 23 (bearing ortho-fluoro substitution) showed ten-fold-enhanced inhibitory potential compared to standard thiourea among category "B" analogs. Molecular docking studies on the active analogs of each category were performed; the results obtained revealed that the presence of hydroxy and fluoro-substitutions on different positions of aryl ring C play a pivotal role in binding interactions with the active site of the targeted urease enzyme.

Whole cell evaluation and the enzymatic kinetic study of urease from ureolytic bacteria affected by potentially toxic elements

Microbially induced carbonate precipitation (MICP) is a biomineralization process that has various applications in environmental pollution remediation and restoration of a range of building materials. In this study, a ureolytic bacterium, Lysinibacillus sp. GY3, isolated from an E-waste site, was found as a promising catalyst for remediation of heavy metals via the MICP process. This bacterial isolate produced significant amounts of urease and showed a great persistence in immobilization of potentially toxic elements. A reference ureolytic strain, Bacillus megaterium VS1, was selected in order to compare the efficiency of Lysinibacillus sp. GY3. Study on urease localization indicated 80 % more urease activity secreted extracellularly as for Lysinibacillus sp. GY3 compared to B. megaterium VS1. From the investigation on effects of metals on both intra- and extra-cellular urease, it was clear that Lysinibacillus sp. GY3 produced the most stable urease under conditions of metal pressure, especially retaining more than 70 % activity in the presence of 1 g/L Pb²⁺ and Zn²⁺. These results suggest that this isolated microorganism could be promisingly introduced in the MICP process to stabilize complex heavy metal pollutions, with reference to the regulating ability under harsh conditions to stabilize urease activity. This species is so important both for its biological features and environmental impacts. In addition, the present study will bring new insight in the field of metal remediation coupled with enzyme engineered biotechnology.

Nitrogen and phosphorus significantly alter growth, nitrogen fixation, anatoxin-a content, and the transcriptome of the bloom-forming cyanobacterium, Dolichospermum

While freshwater cyanobacteria are traditionally thought to be limited by the availability of phosphorus (P), fixed nitrogen (N) supply can promote the growth and/or toxin production of some genera. This study characterizes how growth on N2 (control), nitrate (NO3 -), ammonium (NH4 +), and urea as well as P limitation altered the growth, toxin production, N2 fixation, and gene expression of an anatoxin-a (ATX-A) - producing strain of Dolichospermum sp. 54. The transcriptomes of fixed N and P-limited cultures differed significantly from those of fixed N-deplete, P-replete (control) cultures, while the transcriptomes of P-replete cultures amended with either NH4 + or NO3 - were not significantly different relative to those of the control. Growth rates of Dolichospermum (sp. 54) were significantly higher when grown on fixed N relative to without fixed N; growth on NH4 + was also significantly greater than growth on NO3 -. NH4 + and urea significantly lowered N2 fixation and nifD gene transcript abundance relative to the control while cultures amended with NO3 - exhibited N2 fixation and nifD gene transcript abundance that was not different from the control. Cultures grown on NH4 + exhibited the lowest ATX-A content per cell and lower transcript abundance of genes associated ATX-A synthesis (ana), while the abundance of transcripts of several ana genes were highest under fixed N and P - limited conditions. The significant negative correlation between growth rate and cellular anatoxin quota as well as the significantly higher number of transcripts of ana genes in cultures deprived of fixed N and P relative to P-replete cultures amended with NH4 + suggests ATX-A was being actively synthesized under P limitation. Collectively, these findings indicate that management strategies that do not regulate fixed N loading will leave eutrophic water bodies vulnerable to more intense and toxic (due to increased biomass) blooms of Dolichospermum.

Urea hydrolysis and long-term storage of source-separated urine for reuse as fertiliser is insufficient for the removal of anthropogenic micropollutants

Human and animal source-separated urine, stored and allowed to naturally hydrolyse (the bio-catalysed transformation of urea to ammonia and bicarbonate), has been used for millennia as a fertiliser in agriculture. In a context of growing water scarcity and climate uncertainty, source-separation of urine is facing a strong revival thanks to the emergence of cost-effective waterless collection systems. Concomitantly, urine source-separation can be used as a method for nutrient recovery and subsequent reuse. In its simplest form, such recovery consists of collection followed by urea hydrolysis and storage as sole treatment. Numerous guidelines, including by the World Health Organisation, consider that this is sufficient to stabilise the nutrients and inactivate any potential pathogens in the urine. However, it is still unclear whether said urine is effectively free from other compounds of concern, such as anthropogenic micropollutants with known toxicological effects. Moreover, it is also currently unknown if the metabolites produced by human consumption of these products behave in similar way during short- and long-term storage i.e. whether any changes in chemical structure mean that these could be sorbed and/or precipitated in a different way, or if they can potentially be degraded by the biomass inherently present in urine collection systems. Finally, there is currently no knowledge of whether the observed concentrations of micropollutants in stored hydrolysed urine could potentially have toxicological effects if/when applied to soils and edible crops. To fill these research gaps, 20 commonly consumed compounds were selected in this study and their concentrations in the liquid and solid phases studied in the short- and long-term (up to ≥ 2 years). During the initial process of urea hydrolysis (≤ 5 days), ethyl-glucuronide was the sole compound effectively removed (by deconjugation), while only two other compounds, erythromycin and its metabolite, saw a reduction in their concentration (likely due to biomass sorption). Subsequently, during early storage (≤ 15 days), only three additional compounds were removed: paracetamol (> 99%), acesulfame (11.5%) and carbamazepine-10,11 epoxide (40.7%). Finally, long-term storage of up to 24 months did not result in any further significant removal for any of the measured compounds, indicating that the procedure of hydrolysis + storage is not effective for the removal of anthropogenic micropollutants. The results of this investigation raise strong concerns about the direct reuse of hydrolysed/stored human source-separated urine, and evidence the need for post-processing before implementation as fertiliser into edible crops due to the inherent toxicological risk, particularly to infants.

Three New Acrylic Acid Derivatives from Achillea mellifolium as Potential Inhibitors of Urease from Jack Bean and α-Glucosidase from Saccharomyces cerevisiae

(1) Background: Achillea mellifolium belongs to a highly reputed family of medicinal plants, with plant extract being used as medicine in indigenous system. However, limited data is available regarding the exploitation of the medicinal potential of isolated pure compounds from this family; (2) Methods: A whole plant extract was partitioned into fractions and on the basis of biological activity, an ethyl acetate fraction was selected for isolation of pure compounds. Isolated compounds were characterized using different spectroscopic techniques. The compounds isolated from this study were tested for their medicinal potential using in-vitro enzyme assay, coupled with in-silico studies; (3) Results: Three new acrylic acid derivatives (1–3) have been isolated from the ethyl acetate fraction of Achillea mellifolium. The characterization of these compounds (1–3) was carried out using UV/Vis, FT-IR, 1D and 2D-NMR spectroscopy (¹H-NMR, ¹³C-NMR, HMBC, NOESY) and mass spectrometry. These acrylic acid derivatives were further evaluated for their enzyme inhibition potential against urease from jack bean and α glucosidase from Saccharomyces cerevisiae, using both in-silico and in-vitro approaches. In-vitro studies showed that compound 3 has the highest inhibition against urease enzyme (IC₅₀ =10.46 ± 0.03 μΜ), followed by compound 1 and compound 2 with percent inhibition and IC₅₀ value of 16.87 ± 0.02 c and 13.71 ± 0.07 μΜ, respectively, compared to the standard (thiourea-IC₅₀ = 21.5 ± 0.01 μΜ). The investigated IC₅₀ value of compound 3 against the urease enzyme is two times lower compared to thiourea, suggesting that this compound is twice as active compared to the standard drug. On the other hand, all three compounds (1–3) revealed mild inhibition potential against α-glucosidase. In-silico molecular docking studies, in combination with MD simulations and free energy, calculations were also performed to rationalize their time evolved mode of interaction inside the active pocket. Binding energies were computed using a MMPBSA approach, and the role of individual residues to overall binding of the inhibitors inside the active pockets were also computed; (4) Conclusions: Together, these studies confirm the inhibitory potential of isolated acrylic acid derivatives against both urease and α-glucosidase enzymes; however, their inhibition potential is better for urease enzyme even when compared to the standard.

Flavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis

A sudden outbreak of a novel coronavirus SARS-CoV-2 in 2019 has now emerged as a pandemic threatening to efface the existence of mankind. In absence of any valid and appropriate vaccines to combat this newly evolved agent, there is need of novel resource molecules for treatment and prophylaxis. To this effect, flavonol morin which is found in fruits, vegetables and various medicinal herbs has been evaluated for its antiviral potential in the present study. PASS analysis of morin versus reference antiviral drugs baricitinib, remdesivir and hydroxychloroquine revealed that morin displayed no violations of Lipinski's rule of five and other druglikeness filters. Morin also displayed no tumorigenic, reproductive or irritant effects and exhibited good absorption and permeation through GI (clogP <5). In principal component analysis, morin appeared closest to baricitinib in 3D space. Morin displayed potent binding to spike glycoprotein, main protease 3CLPro and papain-like protease PLPro of SARS-CoV-2, SARS-CoV and MERS-CoV using molecular docking and significant binding to three viral-specific host proteins viz. human ACE2, importin-α and poly (ADP-ribose) polymerase (PARP)-1, further lending support to its antiviral efficacy. Additionally, morin displayed potent binding to pro-inflammatory cytokines IL-6, 8 and 10 also supporting its anti-inflammatory activity. MD simulation of morin with SARS-CoV-2 3CLPro and PLPro displayed strong stability at 300 K. Both complexes exhibited constant RMSDs of protein side chains and Cα atoms throughout the simulation run time. In conclusion, morin might hold considerable therapeutic potential for the treatment and management of not only COVID-19, but also SARS and MERS if studied further. Communicated by Ramaswamy H. Sarma.

Urease and α-Chymotrypsin Inhibitory Activities and Molecular Docking Studies of Alkaloids Isolated from Medicinal Plant Isatis minima Bunge

Phytochemical studies on the alkaloids fraction of the entire plant of Isatis minima Bunge resulted in the alkaloids 1–4 isolation, which were first time isolated from this species. The 1D and 2D NMR spectroscopic data were used to identify their structures, and there was satisfactory compatibility of the data compared to those which were previously published. In the examined compounds 1–4, Isaindigotidione (3) and Isaindigotone (4) were shown as an effective urease inhibitor in such a concentration-dependent way against Jack bean and Bacillus pasteurii urease, with IC₅₀ values 29.03 ± 0.04, 20.04 ± 0.09 and 34.03 ± 0.07, 26.13 ± 0.08 μM, respectively. Compounds 3 and 4 were likewise shown to be an effective inhibitor against α-chymotrypsin, exhibiting IC₅₀ values 16.09 ± 0.07 and 22.01 ± 0.06 μM, correspondingly. The program MOE-Dock was used to perform a molecular docking analysis to confirm probable binding modes of the active complexes of the isolated compounds 1–4 and the crystal structure of urease and α-chymotrypsin enzymes. Compound 3 was the most active, having the highest docking scores against Bacillus pasteurii urease, α-chymotrypsin, and Jack bean (−8.6876), (−7.6647), and (−13.1927) μM, respectively. All four alkaloids (1–4) showed significant urease and protease inhibitory potential and further these activities were confirmed with the help of molecular docking study.

Start-up and performance of a downflow fluidised bed reactor for biological treatment of yellow wastewater and nutrient recovery

The treatment of yellow water (human urine) in a downflow fluidised bed reactor (DFFBR) was investigated to evaluate biological ureolysis and nutrient recovery. The reactor was operated at 30±4 °C in batch mode, and reaction time = 1 d. The average immobilised biomass (as volatile solids, IVS) in the reactor was 2.5±0.9 g L^-1_support, and specific ureolytic activity was 121 g Urea-N g^-1 IVS d^-1. The kinetic parameters were 0.152 mol L^-1 (K_m) and 8 mol g^-1 IVS d^-1 (V_max). The ureolysis efficiency was 93.4% and chemical oxygen demand removal efficiency was 31.2%, while total ammonium nitrogen (NH₄⁺-N) production rate was 7 g L^-1 d^-1 and phosphate removal reached 26%. Precipitates recovery during biological treatment was 1.72±0.8 g. These results suggest that the treatment of yellow water in a DFFBR is a viable option for partial recovery of N and P.

A multicentre study on spontaneous in-cage activity and micro-environmental conditions of IVC housed C57BL/6J mice during consecutive cycles of bi-weekly cage-change

Mice respond to a cage change (CC) with altered activity, disrupted sleep and increased anxiety. A bi-weekly cage change is, therefore, preferred over a shorter CC interval and is currently the prevailing routine for Individually ventilated cages (IVCs). However, the build-up of ammonia (NH₃) during this period is a potential threat to the animal health and the literature holds conflicting reports leaving this issue unresolved. We have therefor examined longitudinally in-cage activity, animal health and the build-up of ammonia across the cage floor with female and male C57BL/6 mice housed four per IVC changed every other week. We used a multicentre design with a standardised husbandry enabling us to tease-out features that replicated across sites from those that were site-specific. CC induce a marked increase in activity, especially during daytime (~50%) when the animals rest. A reduction in density from four to two mice did not alter this response. This burst was followed by a gradual decrease till the next cage change. Female but not male mice preferred to have the latrine in the front of the cage. Male mice allocate more of the activity to the latrine free part of the cage floor already the day after a CC. A behaviour that progressed through the CC cycle but was not impacted by the type of bedding used. Reducing housing density to two mice abolished this behaviour. Female mice used the entire cage floor the first week while during the second week activity in the latrine area decreased. Measurement of NH₃ ppm across the cage floor revealed x3 higher values for the latrine area compared with the opposite area. NH₃ ppm increases from 0–1 ppm to reach ≤25 ppm in the latrine free area and 50–100 ppm in the latrine area at the end of a cycle. As expected in-cage bacterial load covaried with in-cage NH₃ ppm. Histopathological analysis revealed no changes to the upper airways covarying with recorded NH₃ ppm or bacterial load. We conclude that housing of four (or equivalent biomass) C57BL/6J mice for 10 weeks under the described conditions does not cause any overt discomfort to the animals.

Steps towards a nature inspired inorganic crystal engineering

This Perspective outlines the results obtained at the University of Bologna by applying crystal engineering strategies to develop nature inspired organic-inorganic materials to tackle challenges in the health and environment sectors. It is shown by means of a number of examples that co-crystallization of inorganic salts, such as alkali and transition metal halides, with organic compounds, such as amino acids, urea, thiourea and quaternary ammonium salts, can be successfully used for (i) chiral resolution and conglomerate formation from racemic compounds, (ii) inhibition of soil enzyme activity in order to reduce urea decomposition and environmental pollution, and (iii) preparation of novel agents to tackle antimicrobial resistance. All materials described in this Perspective have been obtained by mechanochemical solvent-free or slurry methods and characterized by solid state techniques. The fundamental idea is that a crystal engineering approach based on the choice of intermolecular interactions (coordination and hydrogen bonds) between organic and inorganic compounds allows obtaining materials with collective properties that are different, and often very much superior to those of the separate components. It is also demonstrated that the success of this strategy depends crucially on cross-disciplinary synergistic exchange with expert scientists in the areas of bioinorganics, microbiology, and chirality application-oriented developments of these novel materials.

A quantitative, high-throughput urease activity assay for comparison and rapid screening of ureolytic bacteria

Urease is a dinickel enzyme commonly found in numerous organisms that catalyses the hydrolysis of urea into ammonia and carbon dioxide. The microbially induced carbonate precipitation (MICP) process mediated by urease-producing bacteria (UPB) can be used for many applications including, environmental bioremediation, soil improvement, healing of cracks in concrete, and sealing of rock joints. Despite the importance of urease and UPB in various applications, a quantitative, high-throughput assay for the comparison of urease activity in UPB and rapid screening of UPB from diverse environments is lacking. Herein, we reported a quantitative, 96-well plate assay for urease activity based on the Christensen's urea agar test. Using this assay, we compared urease activity of six bacterial strains (E. coli BL21, P. putida KT2440, P. aeruginosa PAO1, S. oneidensis MR-1, S. pasteurii DSM 33, and B. megaterium DSM 319) and showed that S. pasteurii DSM 33 exhibited the highest urease activity. We then applied this assay to quantify the inhibitory effect of calcium on urease activity of S. pasteurii DSM 33. No significant inhibition was observed in the presence of calcium at concentrations below 10 mM, while the urease activity decreased rapidly at higher concentrations. At a concentration higher than 200 mM, calcium completely inhibited urease activity under the tested conditions. We further applied this assay to screen for highly active UPB from a wastewater enrichment and identified a strain of S. pasteurii exhibiting a substantially higher urease activity than DSM 33. Taken together, we established a 96-well plate-based quantitative, high-throughput urease activity assay that can be used for comparison and rapid screening of UPB. As UPB and urease activity are of interest to environmental, civil, and medical researchers and practitioners, we envisage wide applications of the assay reported in this study.

The Effects of Dietary Crude Protein Level on Ammonia Emissions from Slurry from Lactating Holstein-Friesian Cows as Measured in Open-Circuit Respiration Chambers

Simple Summary

Farmed livestock, particularly dairy cows, are the largest source of ammonia (NH₃) emissions to the atmosphere in Europe and other parts of the developed world. Generally, more than 80% of the total agricultural NH₃ emissions in Europe come from manure slurries (mixtures of urine and faeces) with hydrolysis of urea nitrogen (N) in urine, and ammonification of the organic N fraction in faeces as the two main sources of the NH₃. It is also worth noting that the concentration of these two main sources of NH₃ emissions from manure slurries (particularly urea N in urine) is positively associated with dietary protein content.

Abstract

The effect of dietary crude protein (CP) level on ammonia (NH₃) emissions from slurry from lactating Holstein-Friesian cows was studied. Twenty-four-hour total collections of faeces and urine were made from 24 lactating Holstein-Friesian cows fed four total mixed rations containing 141, 151, 177, and 201 g CP/kg DM (6 cows/diet). The collected urine and faeces from each cow were combined to form 2 kg duplicate slurry samples (weight/weight; fresh basis) according to the proportions in which they were excreted. NH₃ emissions from the slurry samples were measured, during 0–24 and 24–48 h intervals in six open-circuit respiration chambers maintained at two temperatures (8 or 18 °C). NH₃ emissions for the 0–24 and 0–48 h intervals, as well as the average daily emissions, increased linearly with increasing dietary CP level. Increasing the temperature from 8 to 18 °C positively affected NH₃ emissions, but only for the 0–24 h interval. In situations where direct measurements are impossible, NH₃ emissions from slurry can be predicted accurately using equations based on dietary CP level supported by either urinary nitrogen, faeces nitrogen, or both. In summary, increasing dietary CP level linearly increased average daily NH₃ emissions from slurry, with a 5.4 g increase for each 10 g increase in dietary CP.

Effects of the Urease Concentration and Calcium Source on Enzyme-Induced Carbonate Precipitation for Lead Remediation

Heavy metal contamination during the rapid urbanization process in recent decades has notably impacted our fragile environments and threatens human health. However, traditional remediation approaches are considered time-consuming and costly, and the effect sometimes does not meet the requirements expected. The present study conducted test tube experiments to reproduce enzyme-induced carbonate precipitation applied to lead remediation under the effects of urease concentration and a calcium source. Furthermore, the speciation and sequence of the carbonate precipitation were simulated using the Visual MINTEQ software package. The results indicated that higher urease concentrations can assure the availability of CO3 2- during the enzyme-induced carbonate precipitation (EICP) process toward benefiting carbonate precipitation. The calcium source determines the speciation of carbonate precipitation and subsequently the Pb remediation efficiency. The use of CaO results in the dissolution of Pb(OH)2 and, therefore, discharges Pb ions, causing some difficulty in forming the multi-layer structure of carbonate precipitation and degrading Pb remediation. The findings of this study are useful in widening the horizon of applications of the enzyme-induced carbonate precipitation technology to heavy metal remediation.

Effects of bacterial inoculation and calcium source on microbial-induced carbonate precipitation for lead remediation

Heavy metal contamination has caused serious threats to surrounding fragile environments and human health. While the novel microbial-induced carbonate precipitation (MICP) technology in the recent years has been proven effective in improving material mechanical and durability properties, the mechanisms remedying heavy metal contamination still remain unclear. In this study, the potential of applying the MICP technology to the lead remediation under the effects of urease activity and calcium source was explored. The values of OD₆₀₀ corresponding to the ureolytic bacterial activity, electrical conductivity (EC), urease activity (UA) and pH were applied to monitor the degree of urea hydrolysis. Further, the carbonate precipitations that possess different speciations and cannot be distinguished through test tube experiments were reproduced using the Visual MINTEQ software package towards verifying the validity of the proposed simulations, and revealing the mechanisms affecting the lead remediation efficiency. The findings summarised in this work give deep insights into lead-contaminated site remediation engineering.

An overview on the synthetic urease inhibitors with structure-activity relationship and molecular docking

Urease is a kind of enzyme which could be found in various bacteria, fungi, plants, and algae, which can quickly catalyze the hydrolysis of urea into ammonia and carbon dioxide. With the ammonia concentration increasing, the activity of Helicobacter pylori has got an obvious enhancement and leads to mucosal damage in the stomach, gastroduodenal infection, peptic ulcers, and gastric cancer. The infectious diseases caused by Helicobacter pylori can be controlled to a certain extent by inhibiting urease activity with urease inhibitors. Hence, studies of urease inhibitors have attracted great attention all over the world and a variety of effective urease inhibitors have been synthesized in recent years. In this review, we will draw summaries for these inhibitors including urease inhibitory activity, inhibition kinetics, structure-activity relationship, and molecular docking. The collected information is expected to provide rational guidance and effective strategy to develop novel, potent, and safe urease inhibitors for better practical applications in the future.

Incorporation of Optical Density into the Blending Design for a Biocement Solution

The engineering practices for applying the microbial precipitation of carbonates require a design of the blending biocement solution (BCS). The BCS is usually blended with concentrated strains NO-A10, reaction media, such as urea and CaCl2, and a solvent, i.e., water or seawater. To characterize the BCS, the unknown microbial characteristics, such as the cell viability, are complex factors. Therefore, the optical density (OD) was redefined as Rcv OD*, in which OD* was the tentative OD of the BCS used and Rcv was the conversion rate concerning the cell viability. To determine Rcv values, a standard precipitation curve based on the precipitation rate at 24 h was determined. It was found that the curve was expressed by λ1 OD+ λ2 OD2, in which λ1 and λ2 were 8.46 M and -17.633 M, respectively. With this, the Rcv and OD values of unknown BCS were estimated from the results of precipitation tests using arbitrary OD* values. By extending the testing time, the second order term of OD or OD* was negligible. Accordingly, the precipitation amount is expressed as 8.46 OD, in which the OD can be estimated by precipitation tests using arbitrary OD* values of BCSs. Unless the Ca2+ value is dominant, the optimum blending of BCS can be determined by OD. Thus, it is concluded that the blending design of BCS is achieved using 8.46 OD, or 8.46 Rcv OD*, and the standard precipitation curve was defined in this study.

QM/MM Molecular Dynamics Simulations Revealed Catalytic Mechanism of Urease

Urease catalyzes the hydrolysis of urea to form ammonia and carbamate, inducing an overall pH increase that affects both human health and agriculture. Inhibition, mutagenesis, and kinetic studies have provided insights into its enzymatic role, but there have been debates on the substrate binding mode as well as the reaction mechanism. In the present study, we report quatum mechanics-only (QM-only) and quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) calculations on urease that mainly investigate the binding mode of urea and the mechanism of the urease-catalyzed hydrolysis reaction. Comparison between the experimental data and our QM(GFN2-xTB)/MM metadynamics results demonstrates that urea hydrolysis via a complex with bidentate-bound urea is much more favorable than via that with monodentate-bound urea for both nucleophilic attack and the subsequent proton transfer steps. We also indicate that the bidentate coordination of urea fits the active site with a closed conformation of the mobile flap and can facilitate the stabilization of transition states and intermediates by forming multiple hydrogen bonds with certain active site residues.

New acetylphenol-based acyl thioureas broaden the scope of drug candidates for urease inhibition: synthesis, in vitro screening and in silico analysis

Helicobacter pylori urease remains a validated drug target for the eradication of pervasive chronic stomach infection that leads to severe human health diseases such as gastritis and stomach cancer. The increased failure of current treatment protocols because of resistance to broadband antibiotics, severe side effects and low compliance underscore the need for a targeted eradication therapy. Therefore, in the present research, we have developed a new series of acetylphenol-based acyl thioureas that can potentially provide a new template for drug candidates to inhibit urease enzyme. Newly synthesized compounds 7a-j were evaluated for urease inhibitory strength using thiourea as a positive control. In vitro inhibitory results revealed that all the tested compounds were significantly potent than the standard drug. The most active lead 7f competitively inhibited the enzyme and displayed an IC50 value of 0.054 ± 0.002 μM, a ~413-fold strong inhibitory potential than thiourea (IC50 = 22.3 ± 0.031 μM). Various insightful structure-activity relationships were developed showing the key structural requirements for potent inhibitory effects. Molecular docking analysis of 7f inside the active pocket of urease suggested several important interactions with amino acid residues such as ILE411, MET637, ARG439, GLN635, ALA636 and ALA440. Finally, pharmacokinetic properties suggested that the tested derivatives are safe to develop as low-molecular-weight drugs to treat ureolytic bacterial infections.

Investigating the potential for microbially induced carbonate precipitation to treat mine waste

In this study, the feasibility of promoting microbially induced carbonate precipitation (MICP) in mine waste piles by using an environmental bacterial enrichment is explored, with goals to reduce metals and acid leaching. MICP has been explored for remediation applications and stabilization of mine waste. Here, we utilize a native bacterial enrichment to promote MICP on seven mine waste samples with variability in acid production and extent of toxic metal leaching. During fifteen applications of MICP solutions and bacteria on waste rock in bench-scale columns, calcium carbonate formed on grain surfaces within all waste samples, though microscopy revealed uneven distribution of CaCO3 coating. The effluent from acid-producing wastes increased in pH during MICP treatment. MICP performance was evaluated with humidity cell and synthetic precipitation leaching procedure (SPLP) tests. Leaching tests revealed reductions in Cd, Pb and Zn concentrations in leachate of all but one sample, mixed results for Cu, and As increasing in all but one leachate sample after treatment. MICP technology has potential for coating mine waste and reducing release of acid and some metals. This study provides a laboratory assessment of MICP feasibility for stabilizing mine waste in situ and mitigating release of toxic metals into the environment.

The Effect of Calcium Source on Pb and Cu Remediation Using Enzyme-Induced Carbonate Precipitation

Heavy metal contamination not only causes threat to human health but also raises sustainable development concerns. The use of traditional methods to remediate heavy metal contamination is however time-consuming, and the remediation efficiency may not meet the requirements as expected. The present study conducted a series of test tube experiments to investigate the effect of calcium source on the lead and copper removals. In addition to the test tube experiments, numerical simulations were performed using Visual MINTEQ software package considering different degrees of urea hydrolysis derived from the experiments. The remediation efficiency degrades when NH4+ and OH− concentrations are not sufficient to precipitate the majority of Pb2+ and Cu2+. It also degrades when CaO turns pH into highly alkaline conditions. The numerical simulations do not take the dissolution of precipitation into account and therefore overestimate the remediation efficiency when subjected to lower Pb(NO3)2 or Cu(NO3)2 concentrations. The findings highlight the potential of applying the enzyme-induced carbonate precipitation to lead and copper remediations.

Quinazolinone-based hybrids with diverse biological activities: A mini-review

Quinazolinone and quinazoline have been shown different pharmacological activities, namely anticancer, anti-inflammatory, anti-hyperlipidemia, analgesic, antihypertensive, and antibacterial. On the other hand, molecular hybridization is a structural modification technique in the design of new ligands which consist of two or more pharmacologically active molecules in one structure. Therefore, due to the importance of the biological activities of quinazolinones for the development of new therapeutic agents, this review emphasizes current findings on various quinazolinone-based hybrids in medicinal chemistry. Moreover, it highlights the biological activities and structure-activity relationship of these hybrids.

Discovery of urease inhibitory effect of sulfamate derivatives: Biological and computational studies

The discovery of life-changing medicines continues to be the driving force for the rapid exploration and expansion of chemical space, enabling access to innovative small molecules of medicinal importance. These small molecules remain the backbone for modern drug discovery. In this context, the treatment of ureolytic bacterial infections inspires the identification of potent and effective inhibitors of urease, a promising and highly needed target for H. pylori eradication. The present study explores the evaluation of sulfamate derivatives for the inhibition of urease enzyme. The tested compounds showed remarkable inhibitory effect and high level of potency. Compound 1q emerged as the lead inhibitor with an IC₅₀ value of 0.062 ± 0.001 µM, ∼360-fold more potent than thiourea (IC₅₀ = 22.31 ± 0.031 µM). The assessment of various contributing factors towards the inhibition profile allowed for the establishment of diverse structure-activity relationships. Kinetics studies revealed the competitive mode of inhibition of compound 1q while molecular modeling analysis identified various crucial binding interactions with ARG609, ARG439, HIS519, HIS492, HIS593, ALA440, and ALA636 in the active pocket of the enzyme. Finally, the calculated pharmacokinetic properties suggest a promising profile of our potent sulfamate-based urease inhibitors.

Urea transport and hydrolysis in the rumen: A review

Inefficient dietary nitrogen (N) conversion to microbial proteins, and the subsequent use by ruminants, is a major research focus across different fields. Excess bacterial ammonia (NH3) produced due to degradation or hydrolyses of N containing compounds, such as urea, leads to an inefficiency in a host's ability to utilize nitrogen. Urea is a non-protein N containing compound used by ruminants as an ammonia source, obtained from feed and endogenous sources. It is hydrolyzed by ureases from rumen bacteria to produce NH3 which is used for microbial protein synthesis. However, lack of information exists regarding urea hydrolysis in ruminal bacteria, and how urea gets to hydrolysis sites. Therefore, this review describes research on sites of urea hydrolysis, urea transport routes towards these sites, the role and structure of urea transporters in rumen epithelium and bacteria, the composition of ruminal ureolytic bacteria, mechanisms behind urea hydrolysis by bacterial ureases, and factors influencing urea hydrolysis. This review explores the current knowledge on the structure and physiological role of urea transport and ureolytic bacteria, for the regulation of urea hydrolysis and recycling in ruminants. Lastly, underlying mechanisms of urea transportation in rumen bacteria and their physiological importance are currently unknown, and therefore future research should be directed to this subject.

Membrane technologies in toilet urine treatment for toilet urine resource utilization: a review

Membrane technologies have broad potential in methods for separating, collecting, storing, and utilizing urine collected from toilets. Recovering urine from toilets for resource utilization instead of treating it in a sewage treatment plant not only reduces extra energy consumption for the degradation of N and P but also saves energy in chemical fertilizer production, which will contribute to carbon emission reduction of 12.19-17.82 kg kgN -1 in terms of N alone. Due to its high efficiency in terms of volume reduction, water recycling, nutrient recovery, and pollutant removal, membrane technology is a promising technology for resource utilization from urine collected from toilets. In this review, we divide membrane technologies for resource utilization from urine collected from toilets into four categories based on the driving force: external pressure-driven membrane technology, vapor pressure-driven membrane technology, chemical potential-driven membrane technology, and electric field-driven membrane technology. These technologies influence factors such as: recovery targets and mechanisms, reaction condition optimization, and process efficiency, and these are all discussed in this review. Finally, a toilet with source-separation is suggested. In the future, membrane technology research should focus on the practical application of source-separation toilets, membrane fouling prevention, and energy consumption evaluation. This review may provide theoretical support for the resource utilization of urine collected from toilets that is based on membrane technology.

Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition

A few gold compounds were recently found to show antimicrobial properties in vitro, holding great promise for the discovery of new drugs to overcome antibiotic resistance. Here, the inhibition of the bacterial virulence factor urease by four Au(I)-compounds, namely Au(PEt₃)Cl, Au(PEt₃)Br, Au(PEt₃)I and [Au(PEt₃)₂]Cl, obtained from the antiarthritic Au(I)-drug Auranofin and earlier reported to act as antimicrobials, is investigated. The three monophosphino Au(I) complexes showed IC₅₀ values in the 30-100 nM range, while the diphosphino Au(I) complex, though being less active, still showed a IC₅₀ value of 7 μM. The structural basis for this inhibition was provided by solving the crystal structures of urease co-crystallized with Au(PEt₃)I and [Au(PEt₃)₂]Cl: at least two Au(I) ions bind the enzyme in a flap domain involved in the catalysis, thus obliterating enzyme activity. Peculiar changes observed in the two structures reveal implications for the mechanism of soft metal binding and enzyme inactivation.

The complex role of microbial metabolic activity in fossilization

Bacteria play an important role in the fossilization of soft tissues; their metabolic activities drive the destruction of the tissues and also strongly influence mineralization. Some environmental conditions, such as anoxia, cold temperatures, and high salinity, are considered widely to promote fossilization by modulating bacterial activity. However, bacteria are extremely diverse, and have developed metabolic adaptations to a wide range of stressful conditions. Therefore, the influence of the environment on bacterial activity, and of their metabolic activity on fossilization, is complex. A number of examples illustrate that simple, general assumptions about the role of bacteria in soft tissue fossilization cannot explain all preservational pathways: (i) experimental results show that soft tissues of cnidaria decay less in oxic than anoxic conditions, and in the fossil record are found more commonly in fossil sites deposited under oxic conditions rather than anoxic environments; (ii) siderite concretions, which often entomb soft tissue fossils, precipitate due to a complex mixture of sulfate- and iron reduction by some bacterial species, running counter to original theories that iron reduction is the primary driver of siderite concretion growth; (iii) arthropod brains, now widely accepted to be preserved in many Cambrian fossil sites, are one of the first structures to decay in taphonomic experiments, indicating that their fossilization processes are complex and influenced by bacterial activity. In order to expand our understanding of the complex process of bacterially driven soft tissue fossilization, more research needs to be done, on fossils themselves and in taphonomic experiments, to determine how the complex variation in microbial metabolic activity influences decay and mineralization.

High-throughput tandem-microwell assay for ammonia repositions FDA-Approved drugs to inhibit Helicobacter pylori urease

To date, little attempt has been made to develop new treatments for Helicobacter pylori (H. pylori), although the community is aware of the shortage of treatments for H. pylori. In this study, we developed a 192-tandem-microwell-based high-throughput assay for ammonia that is a known virulence factor of H. pylori and a product of urease. We could identify few drugs, that is, panobinostat, dacinostat, ebselen, captan, and disulfiram, to potently inhibit the activity of ureases from bacterial or plant species. These inhibitors suppress the activity of urease via substrate-competitive or covalent-allosteric mechanism, but all except captan prevent the antibiotic-resistant H. pylori strain from killing human gastric cells, with a more pronounced effect than acetohydroxamic acid, a well-known urease inhibitor and clinically used drug for the treatment of bacterial infection. This study offers several bases for the development of new treatments for urease-containing pathogens and to study the mechanism responsible for the regulation of urease activity.

Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere

Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.

Synthesis, predictions of drug-likeness, and pharmacokinetic properties of some chiral thioureas as potent enzyme inhibition agents

A series of chiral thioureas (1 - 17) were synthesized from and tested for their anticholinesterase, tyrosinase, and urease enzyme inhibitor activities. Various phenylisothiocyanates were added to solution of l-cysteine in methanol: water (1 : 1 v/v) at room temperature and stirred for 24 h. The precipitated solid was recrystallized from n-butanol. Pure compounds were characterized by NMR (1H and 13C), FTIR, and CHNS. Tertiary amine containing N-(4-(diethylamino)phenyl)-N'-(2-mercapto-carboxyethanyl)thiourea 17, N-(4-(dimethylamino)phenyl)-N'-(2-mercapto-carboxyethanyl)thiourea 16 and trimethoxy containing N-(3,4,5-trimethoxyphenyl)-N'-(2-mercapto-carboxyethanyl)thiourea 14 were more active than galantamine against AChE and BChE enzymes. In tyrosinase enzyme inhibition activity, compound 14, 10, 12, 6, 13, and 11 exhibited higher tyrosinase inhibitory activity showing IC50 values of 1.1 ± 0.1, 1.5 ± 0.3, 1.6 ± 0.6, 1.9 ± 0.5, 2.2 ± 0.9 and 2.9 ± 0.2 mM, respectively. In urease enzyme inhibition activity assay, 17 showed higher activity. This work demonstrates the pharmacological significance of chiral thiourea derivatives synthesized from l-cysteine and shows their potential. There is a need to perform more in vitro and in vivo biological activities followed by clinical trials to bring such thiourea to the market.

The benefits of autotrophic nitrogen removal from high concentration of urea wastewater through a process of urea hydrolysis and partial nitritation in sequencing batch reactor

For the sake of high efficiency and saving operational cost for high-concentration urea wastewater treatment, a novel two-stage partial nitritation (PN)-anammox process containing simultaneous urea hydrolysis and PN in sequencing batch reactor (SBR) was investigated. Although the influent urea concentration increased from 500 to 1200 mg/L, the SBR simultaneously achieved urea removal efficiency higher than 98% and stable PN with effluent NO₂^--N/NH₄⁺-N ratio of 1.0-1.3 without any extra alkalinity addition. The intracellular hydrolysis was the dominant mechanism for urea removal and persistent free ammonia inhibition on nitrite-oxidizing bacteria was the main reason for nitrite accumulation of 97.92% in SBR. The subsequent anammox reactor showed efficient nitrogen removal performance with average ammonium removal efficiency, nitrogen removal efficiency and maximum nitrogen removal loading rate of 98.08%, 81.45% and 1.05 kg N·m^-3·d^-1 respectively. High-throughput sequencing results indicated Gemmatimonadetes became the most abundant bacterial phylum related to potential intracellular urea hydrolysis and displayed obvious ammonium-oxidizing bacteria enrichment and nitrite-oxidizing bacteria inhibition in SBR, and the dominant anammox bacteria (Candidatus_Kuenenia) in anammox reactor. The proposed process was proven to be promising for high-concentration urea wastewater treatment, facilitating the sustainable development of the urea industry in the future.

Isolation and Characterization of Urease-Producing Soil Bacteria

Urease is an enzyme produced by ureolytic microorganisms which hydrolyzes urea into ammonia and carbon dioxide. Microbial urease has wide applications in biotechnology, agriculture, medicine, construction, and geotechnical engineering. Urease-producing microbes can be isolated from different ecosystems such as soil, oceans, and various geological formations. The aim of this study was to isolate and characterize rapid urease-producing bacteria from Ethiopian soils. Using qualitative urease activity assay, twenty urease-producing bacterial isolates were screened and selected. Among these, three expressed urease at high rates as determined by a conductivity assay. The isolates were further characterized with respect to their biochemical, morphological, molecular, and exoenzyme profile characteristics. The active urease-producing bacterial isolates were found to be nonhalophilic to slightly halophilic neutrophiles and aerobic mesophiles with a range of tolerance towards pH (4.0-10.0), NaCl (0.25-5%), and temperature (20-40°C). According to the API ZYM assays, all three isolates were positive for alkaline phosphatase, leucine aryl amidase, acid phosphatase, and naphthol_AS_BI_phosphohydrolase. The closest described relatives of the selected three isolates (Isolate_3, Isolate_7, and Isolate_11) were Bacillus paramycoides, Citrobacter sedlakii, and Enterobacter bugandensis with 16S rRNA gene sequence identity of 99.0, 99.2, and 98.9%, respectively. From the study, it was concluded that the three strains appear to have a relatively higher potential for urease production and be able to grow under a wider range of growth conditions.

Synthesis, in vitro antiurease, in vivo antinematodal activity of quinoline analogs and their in-silico study

Synthesis of quinoline analogs and their urease inhibitory activities with reference to the standard drug, thiourea (IC₅₀ = 21.86 ± 0.40 µM) are presented in this study. The inhibitory activity range is (IC₅₀ = 0.60 ± 0.01 to 24.10 ± 0.70 µM) which displayed that it is most potent class of urease inhibitor. Analog 1-9, and 11-13 emerged with many times greater antiurease potential than thiourea, in which analog 1, 2, 3, 4, 8, 9, and 11 (IC₅₀ = 3.50 ± 0.10, 7.20 ± 0.20, 1.30 ± 0.10, 2.30 ± 0.10, 0.60 ± 0.01, 1.05 ± 0.10 and 2.60 ± 0.10 µM respectively) were appeared the most potent ones among the series. In this context, most potent analogs such as 1, 3, 4, 8, and 9 were further subjected for their in vitro antinematodal study against C. elegans to examine its cytotoxicity under positive control of standard drug, Levamisole. Consequently, the cytotoxicity profile displayed that analogs 3, 8, and 9 were found with minimum cytotoxic outline at higher concentration (500 µg/mL). All analogs were characterized through ¹H NMR, ¹³C NMR and HR-EIMS. The protein-ligand binding interaction for most potent analogs was confirmed via molecular docking study.

Multiple heavy metals immobilization based on microbially induced carbonate precipitation by ureolytic bacteria and the precipitation patterns exploration

Biomineralization to immobilize the toxic metal has great potential for the bioremediation of multiple heavy metal contamination. In this study, the efficiency of Microbially Carbonate Induced Precipitation (MICP) for several common heavy metals (Cu, Zn, Ni, Cd) in mining areas as well as their precipitation patterns were researched. After urease activity and precipitation ability comparison, Sporosarcina kp-4 and kp-22 were selected for subsequent studies. The removal of Cd was mainly based on the formation of cadmium carbonate induced by bacteria activity, while the removal of Cu was depended on the pH increase generated by the same process. Precipitation contributed to Zn and Ni removal was more complex, which was also based on the MICP process. Removal rates of Cu, Zn, Ni, and Cd (the concentration of all metals was 160 mg/L) reached 75.10%, 98.03%, 59.46% and 96.18%, respectively, within 2 h. For the immobilization of Cu, Zn, Ni and Cd at 160 mg/L, the optimal dosages of bacterial cultured solution were about 0.25 mL, 0.8 mL, 0.5 mL and 0.8 mL, respectively. Minimum inhibitory concentrations (MIC) revealed the toxicity of these heavy metals for MICP bacteria was arrange as: Cd > Zn > Ni > Cu. Our study confirmed that urease-producing bacteria could coprecipitate multiple heavy metals even without the ability tolerate them, and the MICP process was an effective biological approach that was worth investigating further to immobilize multiple heavy metals in ecological restoration.

Study on the spatial distribution of ureolytic microorganisms in farmland soil around tailings with different heavy metal pollution

Ureolytic microorganisms, a kind of microorganism which can secrete urease and decompose urea, have great potential in remediation of soil heavy metals based on microbial induced carbonate precipitation. However, the horizontal and vertical distribution of ureolytic microbial community in heavy metals contaminated soils is poorly understood. In this study, urease genes in agricultural soils surrounding tailings were first investigated using metagenomic in two dimensions: heavy metal pollution (Low-L, Middle-M, High-H) and soil depth (0-20 cm, 20-40 cm, 40-60 cm, 60-80 cm, 80-100 cm). Results showed that the effect of heavy metal concentration on ureolytic microorganisms was indeed significant, while the changes of ureolytic microorganisms with increasing soil depth varied in the vertical direction at the same level of heavy metal contamination. H site had the highest diversity of ureolytic microorganisms except for the topsoil. And at the same heavy metal contamination level, the ureolytic microbial diversity was lower in deeper soils. Proteobacteria, Actinobacteria and Thaumarchaeota (Archaea) were the dominant phyla of ureolytic microorganisms in all three sites, accounting for more than 80% of the total. However, the respond to the heavy metal concentrations of three phyla were different, which were increasing, decreasing and essentially unchanged, respectively. Besides, other environmental factors such as SOM and pH had different effects on ureolytic microorganisms, with Proteobacteria being positively correlated and Actinobacteria being the opposite. Another phenomenon was that Actinobacteria and Verrucomicrobia were biomarkers of group L, which could significantly explain the difference with the other two sites. These results provided valuable information for further research on the response mechanism and remediation of heavy metal pollution by ureolytic microbial system.

Varied-shaped gold nanoparticles with nanogram killing efficiency as potential antimicrobial surface coatings for the medical devices

Medical device-associated infections are a serious medical threat, particularly for patients with impaired mobility and/or advanced age. Despite a variety of antimicrobial coatings for medical devices being explored to date, only a limited number have been introduced for clinical use. Research into new bactericidal agents with the ability to eradicate pathogens, limit biofilm formation, and exhibit satisfactory biocompatibility, is therefore necessary and urgent. In this study, a series of varied-morphology gold nanoparticles in shapes of rods, peanuts, stars and spherical-like, porous ones with potent antibacterial activity were synthesized and thoroughly tested against spectrum of Candida albicans, Pseudomonas aeruginosa, Staphylococcus aureus clinical strains, as well as spectrum of uropathogenic Escherichia coli isolates. The optimization of gold nanoparticles synthesis allowed to develop nanomaterials, which are proved to be significantly more potent against tested microbes compared with the gold nanoformulations reported to date. Notably, their antimicrobial spectrum includes strains with different drug resistance mechanisms. Facile and cost-efficient synthesis of gold nanoparticles, remarkable bactericidal efficiency at nanogram doses, and low toxicity, underline their potential for development as a new coatings, as indicated by the example of urological catheters. The presented research fills a gap in microbial studies of non-spherical gold nanoparticles for the development of antimicrobial coatings targeting multidrug-resistant pathogens responsible for device-associated nosocomial infections.

Co-application of biochar and nitrogen fertilizer reduced nitrogen losses from soil

Combined application of biochar and nitrogen (N) fertilizer has the potential to reduce N losses from soil. However, the effectiveness of biochar amendment on N management can vary with biochar types with different physical and chemical properties. This study aimed to assess the effect of two types of hardwood biochar with different ash contents and cation exchange capacity (CEC) on soil N mineralization and nitrous oxide (N2O) production when applied alone and in combination with N fertilizer. Soil samples collected from a temperate pasture system were amended with two types of biochar (B1 and B2), urea, and urea plus biochar, and incubated for 60 days along with soil control (without biochar or urea addition). Soil nitrate N, ammonium N, ammonia-oxidizing bacteria amoA gene transcripts, and N2O production were measured during the experiment. Compared to control, addition of B1 (higher CEC and lower ash content) alone decreased nitrate N concentration by 21% to 45% during the incubation period while the addition of B2 (lower CEC and higher ash content) alone increased the nitrate N concentration during the first 10 days. Biochar B1 also reduced the abundance of amoA transcripts by 71% after 60 days. Compared to B1 + urea, B2 + urea resulted in a significantly greater initial increase in soil ammonium and nitrate N concentrations. However, B2 + urea had a significantly lower 60-day cumulative N2O emission compared to B1 + urea. Overall, when applied with urea, the biochar with higher CEC reduced ammonification and nitrification rates, while biochar with higher ash content reduced N N2O production. Our study demonstrated that biochar has the potential to enhance N retention in soil and reduce N2O emission when it is applied with urea, but the specific effects of the added biochar depend on its physical and chemical properties.

Selective leaching of copper and zinc from primary ores and secondary mineral residues using biogenic ammonia

With the number of easily accessible ores depleting, alternate primary and secondary sources are required to meet the increasing demand of economically important metals. Whilst highly abundant, these materials are of lower grade with respect to traditional ores, thus highly selective and sustainable metal extraction technologies are needed to reduce processing costs. Here, we investigated the metal leaching potential of biogenic ammonia produced by a ureolytic strain of Lysinibacillus sphaericus on eight primary and secondary materials, comprised of mining and metallurgical residues, sludges and automotive shredder residues (ASR). For the majority of materials, moderate to high yields (30-70%) and very high selectivity (>97% against iron) of copper and zinc were obtained with 1 mol L^-1 total ammonia. Optimal leaching was achieved and further refined for the ASR in a two-step indirect leaching system with biogenic ammonia. Copper leaching was the result of local corrosion and differences in leaching against the synthetic (NH₄)₂CO₃ control could be accounted for by pH shifts from microbial metabolism, subsequently altering free NH₃ required for coordination. These results provide important findings for future sustainable metal recovery technologies from secondary materials.

Marine urease with higher thermostability, pH and salinity tolerance from marine sponge-derived Penicillium steckii S4-4

Urease has a broad range of applications, however, the current studies on urease mainly focus on terrestrial plants or microbes. Thus, it is quite necessary to determine if marine-derived ureases have different characteristics from terrestrial origins since the finding of ureases with superior performance is of industrial interest. In this study, the marine urease produced by Penicillium steckii S4-4 derived from marine sponge Siphonochalina sp. was investigated. This marine urease exhibited a maximum specific activity of 1542.2 U mg protein^-1. The molecular weight of the enzyme was 183 kDa and a single subunit of 47 kDa was detected, indicating that it was a tetramer. The N-terminal amino acid sequence of the urease was arranged as GPVLKKTKAAAV with greatest similarity to that from marine algae Ectocarpus siliculosus. This urease exhibited a K _m of 7.3 mmol L^-1 and a V _max of 1.8 mmol urea min^-1 mg protein^-1. The optimum temperature, pH and salinity are 55 ℃, 8.5 and 10%, respectively. This urease was stable and more than 80% of its maximum specific activity was detected after incubating at 25-60 ℃ for 30 min, pH 5.5-10.0 or 0-25% salinity for 6 h. Compared with the terrestrial urease from Jack bean, this marine urease shows higher thermostability, alkaline preference and salinity tolerance, which extends the potential application fields of urease to a great extent.

Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes

Soft metal ions can inactivate urease, a Ni(II)-dependent enzyme whose hydrolytic activity has significant implications in agro-environmental science and human health. Kinetic and structural studies of the reaction of Canavalia ensiformis urease (JBU) and Sporosarcina pasteurii urease (SPU) with Ag(I) compounds of general formula [Ag(PEt₃)X]₄ (X = Cl, Br, I), and with the ionic species [Ag(PEt₃)₂]NO₃, revealed the role of the Ag(I) ion and its ligands in modulating the metal-enzyme interaction. The activity of JBU is obliterated by the [Ag(PEt₃)X]₄ complexes, with IC₅₀ values in the nanomolar range; the efficiency of the inhibition increases in the Cl^- < Br^- < I^- order. The activity of JBU upon [Ag(PEt₃)₂]NO₃ addition decreases to a plateau corresponding to ca. 60% of the original activity and decreases with time at a reduced rate. Synchrotron X-ray crystallography on single crystals obtained after the incubation of SPU with the Ag(I) complexes yielded high-resolution (1.63-1.97 Å) structures. The metal-protein adducts entail a dinuclear Ag(I) cluster bound to the conserved residues αCys322, αHis323, and αMet367, with a bridging cysteine thiolate atom, a weak Ag^…Ag bond, and a quasi-linear Ag(I) coordination geometry. These observations suggest a mechanism that involves the initial substitution of the phosphine ligand, followed by a structural rearrangement to yield the dinuclear Ag(I) cluster. These findings indicate that urease, in addition to the active site dinuclear Ni(II) cluster, possesses a secondary metal binding site, located on the mobile flap domain, capable of recognizing pairs of soft metal ions and controlling catalysis.