Microbial ureases: significance, regulation, and molecular characterization

In vitro enzymatic, in silico ADME and molecular docking based analysis for the identification of novel bis-indole containing triazine-thiazole hybrids derivatives as promising urease inhibitors

The current study details a sequence of sequential reactions for synthesizing bis-indole-based triazine bearing thiazole derivatives. Several steps were involved in the synthesis of bis-indole-based triazine bearing thiazole derivative. The synthetic reactions were monitored via thin-layer chromatography (TLC). Synthesized compounds were characterized using various spectroscopic techniques, including 1H NMR, 13C NMR, and HR-EIMS. The inhibitory activity against urease enzyme of these synthesized compounds was compared with that of thiourea, a standard drug (IC50 = 9.30 ± 0.20 µM). A range of inhibitory potencies were observed for the synthesized compounds, ranging from moderate to excellent, as follows (IC50 = 5.10 ± 0.40 µM to 29.80 ± 0.20 µM). Analyzing the structure-activity relationship (SAR) provided insight into the results, showing that different substituents had different effects on aromatic rings. Several compounds displayed outstanding inhibitory properties (among those tested were 1, 2, 4, 5, and 6 with IC50 = 6.30 ± 0.80, 5.10 ± 0.40, 5.90 ± 0.50, 8.20 ± 0.10, 8.90 ± 0.60 µM, respectively). Anti-urease evaluation of all the synthesized derivatives was conducted in which the selected compounds have shown remarkable potency compared with the standard drug thiourea (IC50 = 9.30 ± 0.20 µM). Molecular docking analysis was carried out for investigating the better binding sites and distance of the derivatives. Moreover, the drug-like properties were explored by the ADME attributes of the synthesized analogs.

Is bismuth(III) able to inhibit the activity of urease? Puzzling results in the quest for soluble urease complexes for agrochemical and medicinal applications

Bismuth(III) complexes have been reported to act as inhibitors of the enzyme urease, ubiquitously present in soils and implicated in the pathogenesis of several microorganisms. The general insolubility of Bi(III) complexes in water at neutral pH, however, is an obstacle to their utilization. In our quest to improve the solubility of Bi(III) complexes, we selected a compound reported to inhibit urease, namely [Bi(HEDTA)]·2H2O, and co-crystallized it with (i) racemic DL-histidine to obtain the conglomerate [Bi2(HEDTA)2(μ-D-His)2]·6H2O + [Bi2(HEDTA)2(μ-L-His)2]·6H2O, (ii) enantiopure L-histidine to yield [Bi2(HEDTA)2(μ-L-His)2]·6H2O, and (iii) cytosine to obtain [Bi(HEDTA)]·Cyt·2H2O. All compounds, synthesised by mechanochemical methods and by slurry, were characterized in the solid state by calorimetric (DSC and TGA) and spectroscopic (IR) methods, and their structures were determined using powder X-ray diffraction (PXRD) data. All compounds show an appreciable solubility in water, with values ranging from 6.8 mg mL-1 for the starting compound [Bi(HEDTA)]·2H2O to 36 mg mL-1 for [Bi2(HEDTA)2(μ-L-His)2]·6H2O. The three synthesized compounds as well as [Bi(HEDTA)]·2H2O were then tested for inhibition activity against urease. Surprisingly, no enzymatic inhibition was observed during in vitro assays using Canavalia ensiformis urease and in vivo assays using cultures of Helicobacter pylori, raising questions on the efficacy of Bi(III) compounds to counteract the negative effects of urease activity in the agro-environment and in human health.

Design and discovery of urease and Helicobacter pylori inhibitors based on benzofuran/benzothiophene-sulfonate and sulfamate scaffolds for the treatment of ureolytic bacterial infections

A series of sulfonate and sulfamate derivatives bearing benzofuran or benzothiophene scaffold exhibited potent inhibitory effect on urease enzyme. Most of the derivatives exhibited significantly higher potency than thiourea, the standard inhibitor. Compound 1s was identified as the most potent urease inhibitor with an IC50 value of 0.42 ± 0.08 μM, which is 53-fold more potent than thiourea, positive control (IC50 = 22.3 ± 0.031 μM). The docking results further revealed the binding interactions towards the urease active site. Phenotypic screening revealed that compounds 1c, 1d, 1e, 1f, 1j, 1n, and 1t exhibit high potency against H. pylori with MIC values ranging from 0.00625 to 0.05 mM and IC50 values ranging from 0.0031 to 0.0095 mM, much more potent than the positive control, acetohydroxamic acid (MIC and IC50 values were 12.5 and 7.38 mM, respectively). Additional studies were performed to investigate the toxicity of these compounds against the gastric epithelial cell line (AGS) and their selectivity profile against E. coli, and five Lactobacillus species representative of the gut microflora. Permeability characteristics of the most promising derivatives were investigated in Caco-2 cell line. The results indicate that the compounds could be targeted in the GIT only without systemic side effects.

Synergistic inhibition of ureolytic activity and growth of Klebsiella pneumoniae in vitro suggests cobinding of fluoride and acetohydroxamic acid at the urease active site and provides a novel strategy to combat ureolytic bacteria

The ability of ureolytic bacteria to break down stable urea to alkaline ammonia leads to several environmental and health challenges. Ureolytic bacteria such as Helicobacter pylori, Klebsiella pneumoniae, and Proteus mirabilis can become pathogenic and cause persistent infections that can be difficult to treat. Inhibiting urease activity can reduce the growth and pathogenicity of ureolytic bacteria. In the present in vitro study, we investigated the synergistic effects of tannic acid (TA) and the urease inhibitors fluoride (F-) and acetohydroxamic acid (AHA). The concentration of AHA needed for efficient inhibition of the ureolytic activity of K. pneumoniae can be significantly reduced if AHA is coapplied with tannic acid and sodium fluoride (NaF). Thus, only 1.20 μmol l-1 AHA in combination with 0.30 mmol l-1 tannic acid and 0.60 mmol l-1 NaF delayed the onset of ureolytic pH increase by 95.8 % and increased the growth lag phase by 124.3 % relative to untreated K. pneumoniae. At these concentrations, without AHA, TA and NaF increased the onset of the ureolytic pH change by only 37.0 % and the growth lag phase by 52.5 %. The strong inhibition obtained with low concentrations of AHA in triple-compound treatments suggests cobinding of F- and AHA at the urease active site and could reduce the side effects of AHA when it is employed as a drug against e.g. urinary tract infections (UTIs) and blocked catheters. This study reports the basis for a promising novel therapeutic strategy to combat infections caused by ureolytic bacteria and the formation of urinary tract stones and crystalline biofilms on catheters.

Exploration of morpholine-thiophene hybrid thiosemicarbazones for the treatment of ureolytic bacterial infections via targeting urease enzyme: Synthesis, biochemical screening and computational analysis

An important component of the pathogenicity of potentially pathogenic bacteria in humans is the urease enzyme. In order to avoid the detrimental impact of ureolytic bacterial infections, the inhibition of urease enzyme appears to be an appealing approach. Therefore, in the current study, morpholine-thiophene hybrid thiosemicarbazone derivatives (5a-i) were designed, synthesized and characterized through FTIR, 1H NMR, 13C NMR spectroscopy and mass spectrometry. A range of substituents including electron-rich, electron-deficient and inductively electron-withdrawing groups on the thiophene ring was successfully tolerated. The synthesized derivatives were evaluated in vitro for their potential to inhibit urease enzyme using the indophenol method. The majority of compounds were noticeably more potent than the conventional inhibitor, thiourea. The lead inhibitor, 2-(1-(5-chlorothiophen-2-yl)ethylidene)-N-(2-morpholinoethyl)hydrazinecarbothioamide (5g) inhibited the urease in an uncompetitive manner with an IC50 value of 3.80 ± 1.9 µM. The findings of the docking studies demonstrated that compound 5g has a strong affinity for the urease active site. Significant docking scores and efficient binding free energies were displayed by the lead inhibitor. Finally, the ADME properties of lead inhibitor (5g) suggested the druglikeness behavior with zero violation.

A comprehensive account on ethnobotany, phytochemistry and pharmacological insights of genus Celtis

The plants of Celtis L. genus have been traditionally used to cure aches, sore throats, fevers, cancer, sexually transmitted diseases, sexual weakness, diarrhea, stomach problems, amenorrhea, menstrual disorders, kidney stones, and pain. The review aims to give a comprehensive account of the current state of ethnopharmacology, phytochemistry, and biological activities of the Celtis genus, as well as to describe the potential area of future avenues. Information on the Celtis genus was obtained from internet sources such as Google Scholar, Web of Science, PubMed, ScienceDirect, and so on by using appropriate keywords, including ethnobotanical, pharmacological, pharmaceutical, bioactivity, phytochemistry, and botanical features of the Celtis genus. This review identified 14 species in the genus Celtis that have a phytopharmacological investigation, including C.africana Burm. f., C. australis L., C. occidentalis L., C. sinensis Pers., C. philippensis Blanco., C. tetrandra Roxb., C. tessmannii Rendle., C. jessoensis Koidz., C. adolfi-friderici Engl., C. iguanaea (Jacq.) Sarg., C. laevigata Wild., C. pallida Torr., C. zenkeri Engl., and C. tournefortii Lam. This genus contains many classified phytoconstituents, such as terpenoids, organic acids, flavonoids, and volatile compounds. Their extracts and pure substances have been shown to have the same anticancer, antibacterial, anti-inflammatory, antioxidant, hepatoprotective, cardioprotective, urease-inhibiting, and antidiarrheal properties as their traditional uses. In terms of current information on ethnopharmacology, phytochemicals, and pharmacological uses, the data acquired in this review could be beneficial and needed for future research. Some phytoconstituents (for instance, kaempferol, myricetin, quercetin, and eugenol) and extracts (for example, leaves, seeds, and ripe fruits extracts of C. australis) showed tremendous results in preliminary testing with promising antimicrobial, anticancer, and urease inhibitory effects. Further research and clinical investigations are needed to develop them as lead compounds and neutraceuticals, which may provide an advance over traditional medicinal systems.

Proteus mirabilis UreR coordinates cellular functions required for urease activity

A hallmark of Proteus mirabilis infection of the urinary tract is the formation of stones. The ability to induce urinary stone formation requires urease, a nickel metalloenzyme that hydrolyzes urea. This reaction produces ammonia as a byproduct, which can serve as a nitrogen source and weak base that raises the local pH. The resulting alkalinity induces the precipitation of ions to form stones. Transcriptional regulator UreR activates expression of urease genes in a urea-dependent manner. Thus, urease genes are highly expressed in the urinary tract where urea is abundant. Production of mature urease also requires the import of nickel into the cytoplasm and its incorporation into the urease apoenzyme. Urease accessory proteins primarily acquire nickel from one of two nickel transporters and facilitate incorporation of nickel to form mature urease. In this study, we performed a comprehensive RNA-seq to define the P. mirabilis urea-induced transcriptome as well as the UreR regulon. We identified UreR as the first defined regulator of nickel transport in P. mirabilis. We also offer evidence for the direct regulation of the Ynt nickel transporter by UreR. Using bioinformatics, we identified UreR-regulated urease loci in 15 Morganellaceae family species across three genera. Additionally, we located two mobilized UreR-regulated urease loci that also encode the ynt transporter, implying that UreR regulation of nickel transport is a conserved regulatory relationship. Our study demonstrates that UreR specifically regulates genes required to produce mature urease, an essential virulence factor for P. mirabilis uropathogenesis.

IMPORTANCE

Catheter-associated urinary tract infections (CAUTIs) account for over 40% of acute nosocomial infections in the USA and generate $340 million in healthcare costs annually. A major causative agent of CAUTIs is Proteus mirabilis, an understudied Gram-negative pathogen noted for its ability to form urinary stones via the activity of urease. Urease mutants cannot induce stones and are attenuated in a murine UTI model, indicating this enzyme is essential to P. mirabilis pathogenesis. Transcriptional regulation of urease genes by UreR is well established; here, we expand the UreR regulon to include regulation of nickel import, a function required to produce mature urease. Furthermore, we reflect on the role of urea catalysis in P. mirabilis metabolism and provide evidence for its importance.

Root Reduction Caused Directly or Indirectly by High Application of Nitrogen Fertilizer Was the Main Cause of the Decline in Biomass and Nitrogen Accumulation in Citrus Seedlings

Citrus is the largest fruit crop around the world, while high nitrogen (N) application in citrus orchards is widespread in many countries, which results not only in yield, quality and environmental issues but also slows down the establishment of citrus canopies in newly cultivated orchards. Thus, the objective of this study was to investigate the physiological inhibitory mechanism of excessive N application on the growth of citrus seedlings. A pot experiment with the citrus variety Orah (Orah/Citrus junos) at four N fertilization rates (0, 50, 100, and 400 mg N/kg dry soil, denoted as N0, N50, N100, and N400, respectively) was performed to evaluate the changes of root morphology, biomass, N accumulation, enzyme activities, and so on. The results showed that the N400 application significantly reduced the total biomass (from 14.24 to 6.95 g/Plant), N accumulation (from 0.65 to 0.33 g/Plant) and N use efficiency (92.69%) in citrus seedlings when compared to the N100 treatment. The partial least squares pathway model further showed that the decline of biomass and N accumulation by high N application were largely attributed to the reduction of root growth through direct and indirect effects (the goodness of fit under the model was 0.733.) rather than just soil N transformation and activity of root N uptake. These results are useful to optimize N management through a synergistic N absorption and utilization by citrus seedlings.

Genome Sequence Analysis of Calcifying Bacteria Bacillus paranthracis CT5 and Its Biomineralization Efficacy to Improve the Strength and Durability Properties of Civil Structures

Bacteria producing urea amidohydrolases (UA) and carbonic anhydrases (CA) are of great importance in civil engineering as these enzymes are responsible for microbially induced calcium carbonate precipitation (MICCP). In this investigation, genomic insights of Bacillus paranthracis CT5 and the expression of genes underlying in MICCP were studied. B. paranthracis produced a maximum level of UA (669.3 U/ml) and CA (125 U/ml) on 5th day of incubation and precipitated 197 mg/100 ml CaCO3 after 7 days of incubation. After 28 days of curing, compressive strength of bacterial admixed and bacterial cured (B-B) specimens was 13.7% higher compared to water-mixed and water-cured (W-W) specimens. A significant decrease in water absorption was observed in bacterial-cured specimens compared to water-cured specimens after 28 days of curing. For genome analysis, reads were assembled de novo producing 5,402,771 bp assembly with N50 of 273,050 bp. RAST annotation detected six amidohydrolase and three carbonic anhydrase genes. Among 5700 coding sequences found in genome, COG gene annotation grouped 4360 genes into COG categories with highest number of genes to transcription (435 genes), amino acid transport and metabolism (362 genes) along with cell wall/membrane/envelope biogenesis and ion transport and metabolism. KEGG functional classification predicted 223 pathways consisting of 1,960 genes and the highest number of genes belongs to two-component system (101 genes) and ABC transporter pathways (98 genes) enabling bacteria to sense and respond to environmental signals and actively transport various minerals and organic molecules, which facilitate the active transport of molecules required for MICCP.

The Cd immobilization mechanisms in paddy soil through ureolysis-based microbial induced carbonate precipitation: Emphasis on the coexisting cations and metatranscriptome analysis

Microbial induced carbonate precipitation (MICP) can immobilize metals and reduce their bioavailability. However, little is known about the immobilization mechanism of Cd in the presence of soil cations and the triggered gene expression and metabolic pathways in paddy soil. Thus, microcosmic experiments were conducted to study the fractionation transformation of Cd and metatranscriptome analysis. Results showed that bioavailable Cd decreased from 0.62 to 0.29 mg/kg after 330 d due to the MICP immobilization. This was ascribed to the increase in carbonate bound, Fe-Mn oxides bound, and residual Cd. The underlying immobilization mechanisms could be attributed to the formation of insoluble Cd-containing precipitates, the complexation and lattice substitution with carbonate and Fe, Mn and Al (hydr)oxides, and the adsorption on functional group on extracellular polymers of cell. During the MICP immobilization process, up-regulated differential expression urease genes were significantly enriched in the paddy soil, corresponding to the arginine biosynthesis, purine metabolism and atrazine degradation. The metabolic pathway of bacterial chemotaxis, flagellum assembly, and peptidoglycan biosynthesis and the expression of cadA gene related to Cd excretion enhanced Cd resistance of soil microbiome. Therefore, this study provided new insights into the immobilization mechanisms of Cd in paddy soils through ureolysis-based MICP process.

Ammonium release in synthetic and human urine by a urease immobilized nanoconstruct

In this work, we have studied the ability of urease immobilized on glutaraldehyde crosslinked chitosan coated magnetic iron oxide nanoparticles (Urease/GA/CS/MIONPs), for the hitherto unreported comparative hydrolysis of urea in synthetic (SUr) and real human urine (HUr). The prepared Urease/GA/CS/MIONPs were characterized by a combination of Fourier transform infrared spectroscopy (FTIR), field emission-scanning-electron-microscopy (FESEM), energy dispersive X-ray spectroscopy (EDX) and dynamic light scattering (DLS). The nanoconstructs display the highest ammonium ion liberation post-urea hydrolysis in 1/20 or 1/24-fold dilutions of SUr and HUr, respectively. The optimum activity of immobilized urease is observed at pH 7, and the nanoconstructs facilitate efficient urea-hydrolysis till at least 45 °C. Kinetic analysis of the immobilized urease shows km and vmax of 14.81 mM, 12.36 mM, and 18.55 μM min-1 and 10.10 μM min-1, towards SUr and HUr, respectively. The magnetization of the immobilized urease is suitable for reuse across multiple cycles of urea hydrolysis in SUr and HUr. The robust performance of Urease/GA/CS/MIONPs in SUr and HUr is promising for generating ammonium as a useable source of nitrogen from human urine, and underscores the suitability of SUr as a urine mimic for such interventions.

Enhancing the nitrogen and phosphorus content of faecal-derived biochar via adsorption and precipitation from human urine

Urine diversion in toilets is a promising strategy to maximise nutrient recovery and produce low-cost urine-derived fertilisers. There are various methods for nutrient recovery from urine, including precipitation and adsorption onto porous media, such as biochars. This study uses faecal-derived biochars to produce and, for the first time, comprehensively characterise enriched biochar fertilisers with the addition of fully hydrolysed undiluted human urine. The evolution of urea hydrolysis and nutrient content during urine storage was initially investigated over a 6-month storage period and NH4+ adsorption mechanisms studied under varying biochar doses and NH4-N concentrations. The process was further optimised by adding MgO to induce precipitation reactions, enabling the combined recovery of NH4+ and P. For NH4+ adsorption, experimental data exhibited a good fit to both the Freundlich (R2 = 0.989) and Langmuir (R2 = 0.974) isotherm models and the rate of the reaction was well described by a pseudo 2nd order kinetics model (R2 = 0.988). The NH4+ uptake was rapid during the initial 2 h of the reaction and the adsorption process reached completion after 24 h. The NH4-N adsorption capacity of the faecal-derived biochar was 19.8 mg/g and the main adsorption mechanism identified was ion exchange (K+ ↔ NH4+), as confirmed by XRD and ICP-OES. The effect of different biochar doses (0, 25, 50, 100 g/L) and MgO addition scenarios (Mg:P = 0, 1.5, 4) on N and P recovery showed that the combination of MgO (Mg:P = 1.5) with the lower biochar dose (25 g/L) produced the most NP-rich fertiliser product which was easily separated from the urine. Faecal-derived biochar had a limited adsorption capacity for P, with precipitation being the main mechanism for P recovery. When MgO was added to urine, >98% of total P was recovered via precipitation of struvite/struvite-K and substituted hydroxyapatite, as identified via SEM-EDX. Faecal-derived biochar was a successful carrier to recover the P-containing precipitates and facilitate liquid-solid separation after treatment. The findings of this study provide proof-of concept for the systemic management of source separated human excreta and pave the way for the production of marketable waste-derived fertilisers from on-site sanitation systems.

Uncovering the Dynamics of Urease and Carbonic Anhydrase Genes in Ureolysis, Carbon Dioxide Hydration, and Calcium Carbonate Precipitation

The hydration of CO2 suffers from kinetic inefficiencies that make its natural trapping impractically sluggish. However, CO2-fixing carbonic anhydrases (CAs) remarkably accelerate its equilibration by 6 orders of magnitude and are, therefore, "ideal" catalysts. Notably, CA has been detected in ureolytic bacteria, suggesting its potential involvement in microbially induced carbonate precipitation (MICP), yet the dynamics of the urease (Ur) and CA genes remain poorly understood. Here, through the use of the ureolytic bacteriumSporosarcina pasteurii, we investigate the differing role of Ur and CA in ureolysis, CO2 hydration, and CaCO3 precipitation with increasing CO2(g) concentrations. We show that Ur gene up-regulation coincides with an increase in [HCO3-] following the hydration of CO2 to HCO3- by CA. Hence, CA physiologically promotes buffering, which enhances solubility trapping and affects the phase of the CaCO3 mineral formed. Understanding the role of CO2 hydration on the performance of ureolysis and CaCO3 precipitation provides essential new insights, required for the development of next-generation biocatalyzed CO2 trapping technologies.

In Silico Structural and Functional Insight into the Binding Interactions of the Modeled Structure of Watermelon Urease with Urea

Urease (EC 3.5.1.5) is an amidohydrolase. This nickel-dependent metalloenzyme converts urea into NH3 and CO2. Despite their vital role in plants, the structure and function of watermelon (Citrullus lanatus) urease are unknown. We used third- and fourth-generation gene prediction algorithms to annotate the C. lanatus urease sequence in this investigation. The solved urease structure from Canavalia ensiformis (PDB ID: 4GY7) was utilized as a template model to identify the target 3-D model structure of the unknown C. lanatus urease for the first time. Cluretox, the C. lanatus urease intrinsic disordered area identical to Jaburetox, was also found. The C. lanatus urease structure was docked with urea to study atom interaction, amino acid interactions, and binding analyses in the urease-urea complex at 3.5 Å. This study found that amino acids His517, Gly548, Asp631, Ala634, Thr569, His543, Met635, His407, His490, and Ala438 of C. lanatus urease bind urea. To study the molecular basis and mode of action of C. lanatus urease, molecular dynamics simulation was performed and RMSD, RMSF, Rg, SAS, and H-bond analyses were done. The calculated binding free energy (ΔG) for the urea-urease complex at 100 ns using the MM/PBSA method is -7.61 kJ/mol. Understanding its catalytic principles helps scientists construct more efficient enzymes, tailor fertilization to boost agricultural output, and create sustainable waste management solutions.

Fertilizer recovery from source-separated urine by evaporation with a combined process of dehumidification and the addition of absorbent resin supplement

Urine is an ideal resource for producing fertilizer, and processes of volume reduction are promising ways to recover nutrients from urine. Because urea is rapidly hydrolyzed in fresh urine, the stabilization of urine is usually necessary to avoid nitrogen loss during evaporation for fertilizer production. In this work, we investigated a new method about rapid evaporation for non-pretreated urine by dehumidification and addition of absorbent resin supplement (ARS). We obtained the optimum operating parameters, they were: 40 °C of temperature, 40 % of humidity, 460 cm2/ (L urine) of area, and 16.7 g ARS/(L urine). ARS absorbed the urine completely and quickly, and the moisture in the system was collected by the dehumidifier to keep the constant dry treatment area. Formation of a high salt content in the treatment area further inhibited the hydrolysis of urea, and finally, urea crystals were harvested. This study achieved a high water evaporation efficiency of 95 % and a high recovery fraction (92.2 % of nitrogen and 100 % of phosphorus) at a low temperature of 40 °C. The crystals included CO(NH)2 and NH4Cl, which are ideal fertilizers for vegetation. The results of this study demonstrated that dehumidification combined with addition of ARS for source-separated urine dehydration is a cost-effective and green technology for urine nutrition recovery.

Design, synthesis, and biological studies of the new cysteine-N-arylacetamide derivatives as a potent urease inhibitor

Inhibition of Helicobacter pylori urease is an effective method in the treatment of several gastrointestinal diseases in humans. This bacterium plays an important role in the pathogenesis of gastritis and peptic ulceration. Considering the presence of cysteine and N-arylacetamide derivatives in potent urease inhibitors, here, we designed hybrid derivatives of these pharmacophores. Therefore, cysteine-N-arylacetamide derivatives 5a-l were synthesized through simple nucleophilic reactions with good yield. In vitro urease inhibitory activity assay of these compounds demonstrated that all newly synthesized compounds exhibited high inhibitory activity (IC50 values = 0.35-5.83 μM) when compared with standard drugs (thiourea: IC50 = 21.1 ± 0.11 μM and hydroxyurea: IC50 = 100.0 ± 0.01 μM). Representatively, compound 5e with IC50 = 0.35 μM was 60 times more potent than strong urease inhibitor thiourea. Enzyme kinetic study of this compound revealed that compound 5e is a competitive urease inhibitor. Moreover, a docking study of compound 5e was performed to explore crucial interactions at the urease active site. This study revealed that compound 5e is capable to inhibit urease by interactions with two crucial residues at the active site: Ni and CME592. Furthermore, a molecular dynamics study confirmed the stability of the 5e-urease complex and Ni chelating properties of this compound. It should be considered that, in the following study, the focus was placed on jack bean urease instead of H. pylori urease, and this was acknowledged as a limitation.

The exceptional form and function of the giant bacterium Ca. Epulopiscium viviparus revolves around its sodium motive force

Epulopiscium spp. are the largest known heterotrophic bacteria; a large cigar-shaped individual is a million times the volume of Escherichia coli. To better understand the metabolic potential and relationship of Epulopiscium sp. type B with its host Naso tonganus, we generated a high-quality draft genome from a population of cells taken from a single fish. We propose the name Candidatus Epulopiscium viviparus to describe populations of this best-characterized Epulopiscium species. Metabolic reconstruction reveals more than 5% of the genome codes for carbohydrate active enzymes, which likely degrade recalcitrant host-diet algal polysaccharides into substrates that may be fermented to acetate, the most abundant short-chain fatty acid in the intestinal tract. Moreover, transcriptome analyses and the concentration of sodium ions in the host intestinal tract suggest that the use of a sodium motive force (SMF) to drive ATP synthesis and flagellar rotation is integral to symbiont metabolism and cellular biology. In natural populations, genes encoding both F-type and V-type ATPases and SMF generation via oxaloacetate decarboxylation are among the most highly expressed, suggesting that ATPases synthesize ATP and balance ion concentrations across the cell membrane. High expression of these and other integral membrane proteins may allow for the growth of its extensive intracellular membrane system. Further, complementary metabolism between microbe and host is implied with the potential provision of nitrogen and B vitamins to reinforce this nutritional symbiosis. The few features shared by all bacterial behemoths include extreme polyploidy, polyphosphate synthesis, and thus far, they have all resisted cultivation in the lab.

Biofilm formation is correlated with low nutrient and simulated microgravity conditions in a Burkholderia isolate from the ISS water processor assembly

The International Space Station (ISS) Water Processor Assembly (WPA) experiences intermittent dormancy in the WPA wastewater tank during water recycling events which promotes biofilm formation within the system. In this work we aimed to gain a deeper understanding of the impact of nutrient limitation on bacterial growth and biofilm formation under microgravity in support of biofilm mitigation efforts in exploration water recovery systems. A representative species of bacteria that is commonly cultured from the ISS WPA was cultured in an WPA influent water ersatz formulation tailored for microbiological studies. An isolate of Burkholderia contaminans was cultured under a simulated microgravity (SμG) treatment in a vertically rotating high-aspect rotating vessel (HARV) to create the low shear modeled microgravity (LSMMG) environment on a rotating wall vessel (RWV), with a rotating control (R) in the horizontal plane at the predetermined optimal rotation per minute (rpm) speed of 20. Over the course of the growth curve, the bacterial culture in ersatz media was harvested for bacterial counts, and transcriptomic and nutrient content analyses. The cultures under SμG treatment showed a transcriptomic signature indicative of nutrient stress and biofilm formation as compared to the R control treatment. Further analysis of the WPA ersatz over the course of the growth curve suggests that the essential nutrients of the media were consumed faster in the early stages of growth for the SμG treatment and thus approached a nutrient limited growth condition earlier than in the R control culture. The observed limited nutrient response may serve as one element to explain a moderate enhancement of adherent biofilm formation in the SμG treatment after 24 h. While nutrients levels can be modulated, one implication of this investigation is that biofilm mitigation in the ISS environment could benefit from methods such as mixing or the maintenance of minimum flow within a dormant water system in order to force convection and offset the response of microbes to the secondary effects of microgravity.

Crystal engineering: from promise to delivery

Twenty years ago, I wrote a Chem. Commun. feature article entitled "Crystal Engineering: where from? Where to?": an update is in order. In this Highlight I argue that molecular crystal engineering, one of the areas of fast development of the field, has definitely reached the stage of "delivering the goods": new functional materials assembled via non-covalent interactions and/or improved properties of existing materials. As a proof of concept, the crystal engineering approach to tackle two contemporary emergencies, namely, urea fertilizer degradation and development of antimicrobial resistance by pathogens, is discussed and application-driven examples are provided.

Design, Synthesis, Pharmacological Activities, Structure-Activity Relationship, and In Silico Studies of Novel 5-Substituted-2-(morpholinoimino)-thiazolidin-4-ones

This study is aimed to synthesize morpholine- and thiazolidine-based novel 5-(substituted)benzylidene)-2-(morpholinoimino)-3-phenylthiazolidin-4-ones (3-26) and characterized by molecular spectroscopy. The synthesized compounds were subjected to antioxidant activity with anticholinesterase, tyrosinase, and urease inhibition activities and evaluated the structure-activity relationship (SAR) of enzyme inhibition activities. Compound 11 was found to be the most active antioxidant. In anticholinesterase inhibition, compound 12 (IC50: 17.41 ± 0.22 μM) was the most active against AChE, while compounds 3-26 ( except 3, 8, and 17) showed notable activity against BChE. Compounds 17 (IC50: 3.22 ± 0.70 mM), 15 (IC50: 5.19 ± 0.03 mM), 24 (IC50: 7.21 ± 0.27 mM), 23 (IC50: 8.05 ± 0.11 mM), 14 (IC50: 8.10 ± 0.22 mM), 25 (IC50: 8.40 ± 0.64 mM), 26 (IC50: 8.76 ± 0.90 mM), and 22 (IC50: 9.13 ± 0.55 mM) produced higher tyrosinase inhibition activity. In urease inhibition activity, compounds 20 (IC50: 16.79 ± 0.19 μM), 19 (IC50: 18.25 ± 0.50 μM), 18 (IC50: 20.24 ± 0.77 μM), 26 (IC50: 21.51 ± 0.44 μM), 25 (IC50: 21.70 ± 0.06 μM), and 24 (IC50: 22.49 ± 0.11 μM) demonstrated excellent activities. Besides, the molecular docking study was applied to better understand the inhibitory mechanism between (1-26) compounds and enzymes at the molecular level. According to the results of this study, the synthesized compounds exhibited a better binding affinity toward these enzymes compared to the positive control. Further, molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) binding free energy and molecular dynamics (MD) simulation analyses were performed for AChE with compound 26, which showed high inhibitory activity in silico and in vitro studies. In conclusion, novel morpholine and thiazolidine-based derivative compounds may be pharmacologically effective agents for AChE, BChE, tyrosinase, and urease enzymes.

Reinforcement of Different Sands by Low-pH Bio-Mineralization

Different sands have significant influences on MICP reinforcement effects. Using calcium carbonate production and bioflocculation lag period as evaluation criteria, this study investigates the optimal theoretical pH values of bacterial solutions with different concentrations. We reinforced four different sands using MICP at the optimal theoretical pH, and based on permeability, moisture retention, raindrop erosion, wind erosion, penetration, and SEM tests, the influence of sand properties on low-pH MICP reinforcement was analyzed and the low-pH MICP mechanism was revealed. The results indicate the following: (1) The optimal theoretical pH values for bacterial solutions with concentrations of 0.67 × 108 cells/mL, 3 × 108 cells/mL, and 10 × 108 cells/mL are 4.5, 3, and 4, respectively. (2) With 0.67 × 108, 3 × 108, and 10 × 108 cells/mL bacterial solutions, the strength of tailings sand containing calcium salt was 21.15%, 44.42%, and 13.61% higher than that of quartz sand, respectively. The effective reinforcement depth of alkaline reclaimed sand was 10, 8, and 6 mm lower than that of neutral calcareous sand, respectively. The strength of fine tailings sand was 70.41%, 58.04%, and 22.6% higher than that of coarse reclaimed sand. The effective reinforcement depth of fine quartz sand was 6, 4, and 4 mm lower than that of coarse calcareous sand. (3) Low pH temporarily suppresses urease activity, delaying calcium carbonate flocculation and enhancing reinforcement uniformity. To achieve optimal reinforcement effects, adjusting the actual optimal pH values of bacterial solution based on sand properties is essential in engineering applications.

Exploring the Synthetic Chemistry of Phenyl-3-(5-aryl-2-furyl)- 2-propen-1-ones as Urease Inhibitors: Mechanistic Approach through Urease Inhibition, Molecular Docking and Structure-Activity Relationship

Furan chalcone scaffolds belong to the most privileged and promising oxygen-containing heterocyclic class of compounds, which have a wide spectrum of therapeutic applications in the field of pharmaceutics, pharmacology, and medicinal chemistry. This research described the synthesis of a series of twelve novel and seven reported furan chalcone (conventional synthetic approach) analogues 4a-s through the application of microwave-assisted synthetic methodology and evaluated for therapeutic inhibition potential against bacterial urease enzyme. In the first step, a series of nineteen substituted 5-aryl-2-furan-2-carbaldehyde derivatives 3a-s were achieved in moderate to good yields (40-70%). These substituted 5-aryl-2-furan-2-carbaldehyde derivatives 3a-s were condensed with acetophenone via Claisen-Schmidt condensation to furnish 19 substituted furan chalcone scaffolds 4a-s in excellent yields (85-92%) in microwave-assisted synthetic approach, while in conventional methodology, these furan chalcone 4a-s were furnished in good yield (65-90%). Furan chalcone structural motifs 4a-s were characterized through elemental analysis and spectroscopic techniques. These nineteen (19)-afforded furan chalcones 4a-s were screened for urease inhibitory chemotherapeutic efficacy and most of the furan chalcones displayed promising urease inhibition activity. The most active urease inhibitors were 1-phenyl-3-[5-(2',5'-dichlorophenyl)-2-furyl]-2-propen-1-one 4h with an IC50 value of 16.13 ± 2.45 μM, and 1-phenyl- 3-[5-(2'-chlorophenyl)-2-furyl] -2-propen-1-one 4s with an IC50 value of 18.75 ± 0.85 μM in comparison with reference drug thiourea (IC50 = 21.25 ± 0.15 μM). These furan chalcone derivatives 4h and 4s are more efficient urease inhibitors than reference drug thiourea. Structure-activity relationship (SAR) revealed that the 2,5-dichloro 4h and 2-chloro 4s moiety containing furan chalcone derivatives may be considered as potential lead reagents for urease inhibition. The in silico molecular docking study results are in agreement with the experimental biological findings. The results of this study may be helpful in the future drug discovery and designing of novel efficient urease inhibitory agents from this biologically active class of furan chalcones.

Simultaneous Urea and Phosphate Recovery from Synthetic Urine by Electrochemical Stabilization

Urine is a widely available renewable source of nitrogen and phosphorous. The nitrogen in urine is present in the form of urea, which is rapidly hydrolyzed to ammonia and carbonic acid by the urease enzymes occurring in nature. In order to efficiently recover urea, the inhibition of urease must be done, usually by increasing the pH value above 11. This method, however, usually is based on external chemical dosing, limiting the sustainability of the process. In this work, the simultaneous recovery of urea and phosphorous from synthetic urine was aimed at by means of electrochemical pH modulation. Electrochemical cells were constructed and used for urea stabilization from synthetic urine by the in situ formation of OH- ions at the cathode. In addition, phosphorous precipitation with divalent cations (Ca2+, Mg2+) in the course of pH elevation was studied. Electrochemical cells equipped with commercial (Fumasep FKE) and developmental (PSEBS SU) cation exchange membranes (CEM) were used in this study to carry out urea stabilization and simultaneous P-recovery at an applied current density of 60 A m-2. The urea was successfully stabilized for a long time (more than 1 month at room temperature and nearly two months at 4 °C) at a pH of 11.5. In addition, >82% P-recovery could be achieved in the form of precipitate, which was identified as amorphous calcium magnesium phosphate (CMP) by using transmission electron microscopy (TEM).

Design and synthesis of novel anti-urease imidazothiazole derivatives with promising antibacterial activity against Helicobacter pylori

Urease enzyme is a known therapeutic drug target for treatment of Helicobacter pylori infection due to its role in settlement and growth in gastric mucosa. In this study, we designed a new series of sulfonates and sulfamates bearing imidazo[2,1-b]thiazole scaffold that exhibit a potent inhibitory activity of urease enzyme. The most potent compound 2c inhibited urease with an IC50 value of 2.94 ± 0.05 μM, which is 8-fold more potent than the thiourea positive control (IC50 = 22.3 ± 0.031 μM). Enzyme kinetics study showed that compound 2c is a competitive inhibitor of urease. Molecular modeling studies of the most potent inhibitors in the urease active site suggested multiple binding interactions with different amino acid residues. Phenotypic screening of the developed compounds against H. pylori delivered molecules of that possess high potency (1a, 1d, 1h, 2d, and 2f) in comparison to the positive control, acetohydroxamic acid. Additional studies to investigate the selectivity of these compounds against AGS gastric cell line and E. coli were performed. Permeability of the most promising derivatives (1a, 1d, 1h, 2d, and 2f) in Caco-2 cell line, was investigated. As a result, compound 1d presented itself as a lead drug candidate since it exhibited a promising inhibition against urease with an IC50 of 3.09 ± 0.07 μM, MIC value against H. pylori of 0.031 ± 0.011 mM, and SI against AGS of 6.05. Interestingly, compound 1d did not show activity against urease-negative E. coli and exhibited a low permeability in Caco-2 cells which supports the potential use of this compound for GIT infection without systemic effect.

The advantage of a two-stage nitrification method for fertilizer recovery from human urine

Recycling nutrients (nitrogen, phosphorus, and potassium) from human urine can potentially offset more than 13% of global agricultural fertilizer demand. Biological nitrification is a promising method for converting volatile ammonia in high-strength human urine into stable ammonium nitrate (a typical fertilizer), but it is usually terminated in the intermediate production of nitrite due to the inhibition of nitrite-oxidizing bacteria by free nitrous acid (FNA). This study aimed to develop a stable nitrification process in a unique two-stage bioreactor by removing critical barriers associated with FNA inhibition. Experimental results show that half of the ammonium in high-strength urine was successfully converted into nitrate, forming valuable ammonium nitrate (with a nitrogen concentration greater than 1500 mg N/L). The ammonium nitrate solution could retain most phosphorus (75% ± 3%) and potassium (96% ± 1%) in human urine, resulting in nearly full nutrient recovery. Once concentrated, the liquid compound fertilizer of ammonium nitrate was generated. Based on an assessment of economic and environmental impacts at the urban scale, urine diversion for nutrient recovery using a technical combination of nitrification and reverse osmosis could reduce total energy input by 43%, greenhouse gas emission by 40%, and cost by 33% compared to conventional wastewater management. Further research is needed to optimize the two-stage nitrification method on a larger scale.

The Evolving Role of Proteins in Wearable Sweat Biosensors

Sweat is an increasingly popular biological medium for fitness monitoring and clinical diagnostics. It contains an abundance of biological information and is available continuously and noninvasively. Sweat-sensing devices often employ proteins in various capacities to create skin-friendly matrices that accurately extract valuable and time-sensitive information from sweat. Proteins were first used in sensors as biorecognition elements in the form of enzymes and antibodies, which are now being tuned to operate at ranges relevant for sweat. In addition, a range of structural proteins, sometimes assembled in conjunction with polymers, can provide flexible and compatible matrices for skin sensors. Other proteins also naturally possess a range of functionalities─as adhesives, charge conductors, fluorescence emitters, and power generators─that can make them useful components in wearable devices. Here, we examine the four main components of wearable sweat sensors─the biorecognition element, the transducer, the scaffold, and the adhesive─and the roles that proteins have played so far, or promise to play in the future, in each component. On a case-by-case basis, we analyze the performance characteristics of existing protein-based devices, their applicable ranges of detection, their transduction mechanism and their mechanical properties. Thereby, we review and compare proteins that can readily be used in sweat sensors and others that will require further efforts to overcome design, stability or scalability challenges. Incorporating proteins in one or multiple components of sweat sensors could lead to the development and deployment of tunable, greener, and safer biosourced devices.

Inhibited and Retarded Behavior by Ca2+ and Ca2+/OD Loading Rate on Ureolytic Bacteria in MICP Process

The estimation of optical density (OD) with viable cells is challenging for engineering purposes. In this study, the OD conversion based on previous study was used. The inhibited and retarded behavior of the microbially induced carbonate precipitation (MICP) process was examined. The experimental results showed that high Ca²⁺ drastically influences the inhibited and retarded behavior on MICP processes. The analysis showed that the inhibition and retardation effects occurred when the Ca²⁺/OD loading rate exceeded 8.46 M. The critical value was equal to the proportional constant for obtaining carbonate precipitation rate (CPR) from OD. Due to this, the blending design of materials became possible, with no risk of inhibition. In conclusion, the inhibition and retardation of the MICP process are governed by the Ca²⁺ load and the linear standard line (LSL), which may be attributed to the capacity or tolerance of viable cells, i.e., CPR/OD = 8.46 M or Ca²⁺/OD = 8.46 M.

An Improved Method for Determining Urease Activity from Electrical Conductivity Measurements

We present an improved approach to evaluating the activity of urease from electrical conductivity (EC) measurements. In this approach, chemical equilibrium modeling via PHREEQC is used in conjunction with empirical equations for computing EC to develop a function that relates the increase in EC during urea hydrolysis in a closed reactor to the concentration of ammonium species present (and concentration of urea remaining) in the reaction solution. By applying this function to data from continuous measurement of EC during urea hydrolysis, we obtain a profile of the concentration of the urea substrate with time, which is then used to determine the urease activity. The activity of commercially available urease extracted from jack beans was determined using this method and compared well to the activity determined using Nessler's reagent, a commonly used colorimetric assay. This EC-based method is inexpensive and can be used for accurate determination of urease activity for a variety of applications.

Five decades of metalloenzymology

Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.

The Ability of Streptococcus thermophilus BT01 to Modulate Urease Activity in Healthy Subjects' Fecal Samples Depends on the Biomass Production Process

SCOPE

This study evaluates how manufacturing conditions of probiotic biomass production, using two different cryoprotectants, Cryo-A and Cryo-B, can affect Streptococcus thermophilus BT01 in vivo gastrointestinal tract survival and its ability to modulate the level of urease activity in fecal samples of healthy subjects.

METHODS AND RESULTS

A randomized controlled cross-over study is carried out on 20 adult healthy subjects to evaluate total and viable loads, persistence of S. thermophilus BT01, and urease activity in fecal samples. Strain-specific quantification by using developed culture-based method and molecular qPCR tool allows to quantify viable S. thermophilus BT01 strain in 90% of the subjects. The quantification of both total DNA and recovered viable S. thermophilus BT01 in fecal samples does not reveal significant differences between Cryo-A or Cryo-B treated biomass. However, the administration of S. thermophilus BT01 produced with Cryo-A results in a decreased urease activity in fecal samples compared to Cryo-B protected cells.

CONCLUSION

This study i) highlights how the manufacturing conditions can play a role in influencing the probiotic functionality in vivo and ii) represents the first evidence that links S. thermophilus to a specific probiotic mechanism, the reduction of urease activity in fecal samples.

Immobilizing of lead and copper using chitosan-assisted enzyme-induced carbonate precipitation

Enzyme-induced carbonate precipitation (EICP) is considered as an environmentally friendly method for immobilizing heavy metals (HMs). The fundamental of the EICP method is to catalyze urea hydrolysis using the urease, discharging CO₃^2- and NH₄⁺. CO₃^2- helps to form carbonates that immobilize HMs afterwards. However, HMs can depress urease activity and reduce the degree of urea hydrolysis. Herein, the potential of applying the chitosan-assisted EICP method to Pb and Cu immobilization was explored. The chitosan addition elevated the degree of urea hydrolysis when subjected to the effect of Cu²⁺ toxicity where the protective effect, flocculation and adsorption, and the formation of precipitation, play parts in improving the Cu immobilization efficiency. The use of chitosan addition, however, also causes the side effect (copper-ammonia complex formation). Two calcium source additions, CaCl₂ and Ca(CH₃COO)₂, intervened in the test tube experiments not only to prevent pH from raising to values where Cu²⁺ complexes with NH₃ but also to separate the urease enzyme and Cu²⁺ from each other with the repulsion of charges. The FTIR spectra indicate that the chitosan addition adsorbs Cu²⁺ through its surface hydroxyl and carboxyl groups, while the SEM images distinguish who the mineral are nucleating with. The findings shed light on the potential of applying the chitosan-assisted EICP method to remedy lead- and copper-rich water bodies.

Application of urease-producing microbial community in seawater to dust suppression in desert

In order to solve the dust problem caused by sandstorms, this paper aims to propose a new method of enriching urease-producing microbial communities in seawater in a non-sterile environment. Besides, the difference of dust suppression performance of enriched microorganisms under different pH conditions was also explored to adapt the dust. The Fourier-transform infrared spectrometry (FTIR) and Scanning electron microscopy (SEM) confirmed the formation of CaCO₃. The X-ray diffraction (XRD) further showed that the crystal forms of CaCO₃ were calcite and vaterite. When urease activity was equivalent, the alkaline environment was conducive to the transformation of CaCO₃ to more stable calcite. The mineralization rate at pH = 10 reached the maximum value on the 7^th day, which was 97.49 ± 1.73%. Moreover, microbial community analysis results showed that the relative abundance of microbial community structure was different under different pH enrichment. Besides, the relative abundance of Sporosarcina, a representative genus of urease-producing microbial community, increased with the increase of pH under culture conditions, which consistent with the mineralization performance results. In addition, the genus level species network diagram also showed that in the microbial community, Sporosarcina was negatively correlated with another urease-producing genus Bacillus, and had a reciprocal relationship with Atopostipes, which means that the urease-producing microbial community was structurally stable. The enrichment of urease-producing microbial communities in seawater will provide empirical support for the large-scale engineering application of MICP technology in preventing and controlling sandstorms in deserts.

Bacteroid Development, Transcriptome, and Symbiotic Nitrogen-Fixing Comparison of Bradyrhizobium arachidis in Nodules of Peanut (Arachis hypogaea) and Medicinal Legume Sophora flavescens

Bradyrhizobium arachidis strain CCBAU 051107 could differentiate into swollen and nonswollen bacteroids in determinate root nodules of peanut (Arachis hypogaea) and indeterminate nodules of Sophora flavescens, respectively, with different N2 fixation efficiencies. To reveal the mechanism of bacteroid differentiation and symbiosis efficiency in association with different hosts, morphologies, transcriptomes, and nitrogen fixation efficiencies of the root nodules induced by strain CCBAU 051107 on these two plants were compared. Our results indicated that the nitrogenase activity of peanut nodules was 3 times higher than that of S. flavescens nodules, demonstrating the effects of rhizobium-host interaction on symbiotic effectiveness. With transcriptome comparisons, genes involved in biological nitrogen fixation (BNF) and energy metabolism were upregulated, while those involved in DNA replication, bacterial chemotaxis, and flagellar assembly were significantly downregulated in both types of bacteroids compared with those in free-living cells. However, expression levels of genes involved in BNF, the tricarboxylic acid (TCA) cycle, the pentose phosphate pathway, hydrogenase synthesis, poly-β-hydroxybutyrate (PHB) degradation, and peptidoglycan biosynthesis were significantly greater in the swollen bacteroids of peanut than those in the nonswollen bacteroids of S. flavescens, while contrasting situations were found in expression of genes involved in urea degradation, PHB synthesis, and nitrogen assimilation. Especially higher expression of ureABEF and aspB genes in bacteroids of S. flavescens might imply that the BNF product and nitrogen transport pathway were different from those in peanut. Our study revealed the first differences in bacteroid differentiation and metabolism of these two hosts and will be helpful for us to explore higher-efficiency symbiosis between rhizobia and legumes. IMPORTANCE Rhizobial differentiation into bacteroids in leguminous nodules attracts scientists to investigate its different aspects. The development of bacteroids in the nodule of the important oil crop peanut was first investigated and compared to the status in the nodule of the extremely promiscuous medicinal legume Sophora flavescens by using just a single rhizobial strain of Bradyrhizobium arachidis, CCBAU 051107. This strain differentiates into swollen bacteroids in peanut nodules and nonswollen bacteroids in S. flavescens nodules. The N2-fixing efficiency of the peanut nodules is three times higher than that of S. flavescens. By comparing the transcriptomes of their bacteroids, we found that they have similar gene expression spectra, such as nitrogen fixation and motivity, but different spectra in terms of urease activity and peptidoglycan biosynthesis. Those altered levels of gene expression might be related to their functions and differentiation in respective nodules. Our studies provided novel insight into the rhizobial differentiation and metabolic alteration in different hosts.

Insights into the genome of Methylobacterium sp. NMS14P, a novel bacterium for growth promotion of maize, chili, and sugarcane

A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium, and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium-type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium-based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.

Flavonoids and related privileged scaffolds as potential urease inhibitors: a review

Infections caused by bacteria are a significant issue on a global scale, and imperative action is required to discover novel or improved therapeutic agents. Flavonoids are a class of plant-derived compounds that have a variety of potentially useful bioactivities. These activities include immediate antimicrobial properties, synergistic effect with antimicrobials, ferocious repression of pathogenicity, anti-urease activity etc. This review summarizes current studies concerning anti-urease actions of flavonoids as well as structural-activity correlation investigations of the flavonoid core structure. It is possible that if researchers investigate the many structural changes that may be made in flavonoid rings, they'll be able to build up novel compounds that have powerful and effective anti-urease properties.

Effect of salivary urea, pH and ureolytic microflora on dental calculus formation and its correlation with periodontal status

Context

Dental calculus, formed by mineralization of plaque predisposes to the development of periodontal disease.

Aim

To evaluate the influence of salivary urea and the presence of ureolytic bacteria on dental calculus formation and periodontal status in patients with good, fair and poor oral hygiene.

Material and methods

An observational cross-sectional study was carried out on 135 patients, 18–60 years of age. Based on the simplified calculus index, patients were divided into three groups, good oral hygiene, fair oral hygiene and poor oral hygiene. Clinical parameters such as plaque index, gingival index, pocket probing depth and clinical attachment level and salivary pH were recorded for each subject. Saliva samples were collected to evaluate the urea levels using autoanalyzer method. Supragingival calculus samples were collected and presence and quantification of ureolytic bacteria were done by gram staining and bacterial culture and confirmed by biochemical reaction. For statistical analysis, test like Shapiro-Wilk test, Kruskal Wallis and Spearman's rho were used.

Results

Increase in salivary pH was associated with increased odds of higher calculus index score (odds ratio = 2.785). There was a non-significant weak correlation between salivary urea and ureolytic bacteria in dental calculus in all the three groups (p > 0.05). Higher calculus index score was associated with increased odds of presence of ureolytic bacteria (odds ratio>1).

Conclusions

Higher level of ureolytic bacteria with increasing calculus index score may breakdown the salivary urea to ammonia resulting in a ureolytic pH rise that facilitate calcium phosphate saturation leading to more calculus formation.

An integrated strategy for nutrient harvesting from hydrolyzed human urine as high-purity products: Tracking of precipitation transformation and precise regulation

The nutrient recovery from source-separated urine is of great significance for a sustainable and closed nutrient loop. However, common urine-processing techniques have several constraints, including inefficient recovery, low product purity and incapability of simultaneously harvesting multiple nutrients. In this study, an integrated strategy of P precipitation and N stripping was first proposed to harvest nutrients from hydrolyzed human urine as high-purity products via precisely regulating Ca/P dosing ratio. Ca(OH)2 was utilized to trigger Ca-P precipitation and elevate pH level. Different from the previously reported conventional struvite method, P recovery was oriented to calcium phosphate. P harvesting behavior was investigated as a function of key factors including initial P concentration and the dosing ratio. A thermodynamic model was constructed to unveil the precipitation transformation mechanism and visualize P recovery for an enhanced controllability. For N harvesting, Ca(OH)2 was dosed to increase the pH of the urine to converts ammonium to ammonia. The resulting ammonia was stripped and then adsorbed by H2SO4 as high-purity ammonium sulfate. Moreover, the sulfate derived from acidification treatment was recovered as calcium sulfate in the interests of material recycling and mitigating secondary contaminations. Results exhibited P recovery efficiency could reach 100 % and purity for calcium phosphate could be above 90 % within a Ca/P ratio range of 1.67-2.0. Further boosting pH to 12, over 85 % of S and 95 % of N was retrieved. The comprehensive scheme provides an efficient approach towards the precise P and N harvesting from hydrolyzed urine and advances the knowledge of precipitation transformation mechanism.

Potential of Medicago sativa and Perilla frutescens for overcoming the soil sickness caused by ginseng cultivation

There are serious soil sickness in ginseng cultivation. Crop rotation is an effective agricultural management to improve soil sustainability and reduce soil sickness. To explore an appropriate ginseng rotation system, Medicago sativa (alfalfa) and Perilla frutescens (perilla) were planted on ginseng cultivation soil for 1 year to evaluate the improvement effect of both. Through chemical analysis and high-throughput sequencing technology, we found that after alfalfa and perilla cultivation for one-year, various nutrients and enzyme activities in ginseng cultivation soil were significantly improved. In addition, perilla significantly increased the diversity and richness of soil fungal communities. Cultivation of alfalfa and perilla significantly changed the composition of soil bacterial and fungal communities and significantly reduced the abundance of the potentially pathogenic fungi Ilyonectria. Further pot experiments also showed that the improved soil could significantly increase root activity of ginseng plant after two plants were planted. It should be noted that, unlike alfalfa, perilla decreased soil electrical conductivity, increased soil organic matter, soil urease, and may significantly improve the diversity and richness of soil fungal community. Moreover, in the pot experiment, the root fresh weight of ginseng cultured in perilla treated soil increased significantly. This study highlights that perilla may have better soil improvement effect than alfalfa and it has the potential to be used in the soil improvement of ginseng cultivation.

Membrane Technologies for Nitrogen Recovery from Waste Streams: Scientometrics and Technical Analysis

The concerns regarding the reactive nitrogen levels exceeding the planetary limits are well documented in the literature. A large portion of anthropogenic nitrogen ends in wastewater. Nitrogen removal in typical wastewater treatment processes consumes a considerable amount of energy. Nitrogen recovery can help in saving energy and meeting the regulatory discharge limits. This has motivated researchers and industry professionals alike to devise effective nitrogen recovery systems. Membrane technologies form a fundamental part of these systems. This work presents a thorough overview of the subject using scientometric analysis and presents an evaluation of membrane technologies guided by literature findings. The focus of nitrogen recovery research has shifted over time from nutrient concentration to the production of marketable products using improved membrane materials and designs. A practical approach for selecting hybrid systems based on the recovery goals has been proposed. A comparison between membrane technologies in terms of energy requirements, recovery efficiency, and process scale showed that gas permeable membrane (GPM) and its combination with other technologies are the most promising recovery techniques and they merit further industry attention and investment. Recommendations for potential future search trends based on industry and end users' needs have also been proposed.

X-ray Structures and Computational Studies of Two Bioactive 2-(Adamantane-1-carbonyl)-N-substituted Hydrazine-1-carbothioamides

Two biologically active adamantane-linked hydrazine-1-carbothioamide derivatives, namely 2-(adamantane-1-carbonyl)-N-(tert-butyl)hydrazine-1-carbothioamide) 1 and 2-(adamantane-1-carbonyl)-N-cyclohexylhydrazine-1-carbothioamide 2, have been synthesized. X-ray analysis was conducted to study the effect of the t-butyl and cyclohexyl moieties on the intermolecular interactions and conformation of the molecules in the solid state. X-ray analysis reveals that compound 1 exhibits folded conformation, whereas compound 2 adopts extended conformation. The Hirshfeld surface analysis indicates that the contributions of the major intercontacts involved in the stabilization of the crystal structures do not change much as a result of the t-butyl and cyclohexyl moieties. However, the presence and absence of these contacts is revealed by the 2D-fingerprint plots. The CLP-Pixel method was used to identify the energetically significant molecular dimers. These dimers are stabilized by different types of intermolecular interactions such as N-H···S, N-H···O, C-H···S, C-H···O, H-H bonding and C-H···π interactions. The strength of these interactions was quantified by using the QTAIM approach. The results suggest that N-H···O interaction is found to be stronger among other interactions. The in vitro assay suggests that both compounds 1 and 2 exhibit urease inhibition potential, and these compounds also display moderate antiproliferative activities. Molecular docking analysis shows the key interaction between urease enzyme and title compounds.

Graphene oxide decreases the abundance of nitrogen cycling microbes and slows nitrogen transformation in soils

Graphene oxide (GO) has been widely used in many applications due to its excellent properties. Given the extensive production and use of this nanomaterial, its release into the environment is inevitable. However, little is known about the effects of GO on microbial nitrogen transformation and the related processes after GO enters the soil environment. The present study showed that GO significantly reduced soil microbial biomass and caused a decline in microbial diversity after the soils were subjected to various GO concentrations (10, 100, and 1000 mg kg^-1) for 4 months. Among them, the abundances of nitrogen transformation related bacteria such as Firmicutes, Nitrospirota, Proteobacteria, Planctomycetota, and Cyanobacteria were significantly decreased with GO incubation. Among the enzymes that are related to nitrogen transformation, nitrate reductase was the most sensitive even at low concentrations of GO, followed by ammonia monooxygenase and urease, which were reduced by 13-31%, 5-26%, and 9-19% respectively, than those of the control. We found that high concentrations of GO significantly increased the retention of soil urea by 32-59%, and the contents of ammonium and nitrate were 22-28% and 55-69% lower compared to those of the control, respectively. Moreover, the response of most of the indicators in the above process to multilayer GO was more significant than that to single layer GO. Overall, this study provides new insights into the comprehensive understanding of GO's impacts on the soil nitrogen cycle.

Inhibition of Urease by Hydroquinones: A Structural and Kinetic Study

Hydroquinones are a class of organic compounds abundant in nature that result from the full reduction of the corresponding quinones. Quinones are known to efficiently inhibit urease, a Ni^II -containing enzyme that catalyzes the hydrolysis of urea to yield ammonia and carbonate and acts as a virulence factor of several human pathogens, in addition to decreasing the efficiency of soil organic nitrogen fertilization. Here, we report the molecular characterization of the inhibition of urease from Sporosarcina pasteurii (SPU) and Canavalia ensiformis (jack bean, JBU) by 1,4-hydroquinone (HQ) and its methyl and tert-butyl derivatives. The 1.63-Å resolution X-ray crystal structure of the SPU-HQ complex discloses that HQ covalently binds to the thiol group of αCys322, a key residue located on a mobile protein flap directly involved in the catalytic mechanism. Inhibition kinetic data obtained for the three compounds on JBU reveals the occurrence of an irreversible inactivation process that involves a radical-based autocatalytic mechanism.

A literature review on the potential clinical implications of streptococci in gastric cancer

Streptococcus is widely found in nature and the human body, and most species are not pathogenic. In recent years, studies have found that Streptococcus is associated with gastric cancer. Streptococcus was found to be enriched in the oral cavity, stomach and intestine of gastric cancer patients and found to be increased in gastric cancer tissues, suggesting that Streptococcus may be the pathogenic bacteria underlying gastric cancer. This review discusses the discovery of Streptococcus, the relationship between Streptococcus and gastric cancer, and the possible carcinogenic mechanism of Streptococcus and summarizes the progress of the research on the role of Streptococcus in gastric cancer to provide new ideas for the early detection, diagnosis and treatment of gastric cancer.

Integrated application of bacterial carbonate precipitation and silicon nanoparticles enhances productivity, physiological attributes, and antioxidant defenses of wheat (Triticum aestivum L.) under semi-arid conditions

The use of calcium carbonate-precipitating bacteria (CCPB) has become a well-established ground-improvement technique. However, the effect of the interaction of CCPB with nanoparticles (NPs) on plant performance is still meager. In this study, we aimed at evaluating the role of CCPB and/or silicon NPs (Si-NPs) on the growth, physio-biochemical traits, and antioxidative defense of wheat (Triticum aestivum L.) under semi-arid environmental conditions. A 2-year pot experiment was carried out to determine the improvement of the sandy soil inoculated with CCPB and the foliar application of Si-NPs on wheat plants. We tested the following treatments: spraying plants with 1.0 or 1.5 mM Si-NPs (control = 0 mM Si-NPs), soil inoculated with Bacillus lichenforms (MA16), Bacillus megaterium (MA27), or Bacillus subtilis (MA34), and the interaction of individual Bacillus species with Si-NPs. Our results showed that soil inoculation with any of the three isolated CCPB and/or foliar application of Si-NPs at the rates of 1.0 or 1.5 mM significantly improved (p ≤ 0.05) the physiological and biochemical attributes as well as the enzymatic antioxidant activities of wheat plants. Therefore, the combined treatments of CCPB + Si-NPs were more effective in enhancing physio-biochemical characteristics and enzymatic antioxidant activities than the individual treatments of CCPB or Si-NPs, thus achieving the best performance in the treatment of MA34 + 1.5 mM Si-NPs. Our results demonstrated that the co-application of CCPB and Si-NPs, particularly MA34 + 1.5 mM Si-NPs, considerably activated the antioxidant defense system to mitigate the adverse effects of oxidative stress, thus increasing tolerance and enhancing the production of wheat plants in sandy soils under semi-arid environmental conditions.

Synthesis, Biophysical Interaction of DNA/BSA, Equilibrium and Stopped-Flow Kinetic Studies, and Biological Evaluation of bis(2-Picolyl)amine-Based Nickel(II) Complex

Reaction of bis(2-picolyl)amine (BPA) with Ni(II) salt yielded [(BPA)NiCl2(H2O)] (NiBPA). The Ni(II) in NiBPA bound to a BPA ligand, two chloride, and one aqua ligands. Because most medications inhibit biological processes by binding to a specific protein, the stopped-flow technique was used to investigate DNA/protein binding in-vitro, and a mechanism was proposed. NiBPA binds to DNA/protein more strongly than BPA via a static quenching mechanism. Using the stopped-flow technique, a mechanism was proposed. BSA interacts with BPA via a fast reversible step followed by a slow irreversible step, whereas NiBPA interacts via two reversible steps. DNA, on the other hand, binds to BPA and NiBPA via the same mechanism through two reversible steps. Although BSA interacts with NiBPA much faster, NiBPA has a much higher affinity for DNA (2077 M) than BSA (30.3 M). Compared to NiBPA, BPA was found to form a more stable BSA complex. When BPA and NiBPA bind to DNA, the Ni(II) center was found to influence the rate but not the mechanism, whereas, for BSA, the Ni(II) center was found to change both the mechanism and the rate. Additionally, NiBPA exhibited significant cytotoxicity and antibacterial activity, which is consistent with the binding constants but not the kinetic stability. This shows that in our situation, biological activity is significantly more influenced by binding constants than by kinetic stability. Due to its selectivity and cytotoxic activity, complex NiBPA is anticipated to be used in medicine.

Synthesis and Identification of New N,N-Disubstituted Thiourea, and Thiazolidinone Scaffolds Based on Quinolone Moiety as Urease Inhibitor

Synthesis of thiazolidinone based on quinolone moiety was established starting from 4-hydroxyquinol-2-ones. The strategy started with the reaction of ethyl bromoacetate with 4-hydroxyquinoline to give the corresponding ethyl oxoquinolinyl acetates, which reacted with hydrazine hydrate to afford the hydrazide derivatives. Subsequently, hydrazides reacted with isothiocyanate derivatives to give the corresponding N,N-disubstituted thioureas. Finally, on subjecting the N,N-disubstituted thioureas with dialkyl acetylenedicarboxylates, cyclization occurred, and thiazolidinone derivatives were obtained in good yields. The two series based on quinolone moiety, one containing N,N-disubstituted thioureas and the other containing thiazolidinone functionalities, were screened for their in vitro urease inhibition properties using thiourea and acetohydroxamic acid as standard inhibitors. The inhibition values of the synthesized thioureas and thiazolidinones exhibited moderate to good inhibitory effects. The structure-activity relationship revealed that N-methyl quinolonyl moiety exhibited a superior effect, since it was proved to be the most potent inhibitor in the present series achieving (IC₅₀ = 1.83 ± 0.79 µM). The previous compound exhibited relatively much greater activity, being approximately 12-fold more potent than thiourea and acetohydroxamic acid as references. Molecular docking analysis showed a good protein-ligand interaction profile against the urease target (PDBID: 4UBP), emphasizing the electronic and geometric effect of N,N-disubstituted thiourea.