A methanotrophic bacterium to enable methane removal for climate mitigation.

The rapid increase of the potent greenhouse gas methane in the atmosphere creates great urgency to develop and deploy technologies for methane mitigation. One approach to removing methane is to use bacteria for which methane is their carbon and energy source (methanotrophs). Such bacteria naturally convert methane to CO2 and biomass, a value-added product and a cobenefit of methane removal. Typically, methanotrophs grow best at around 5,000 to 10,000 ppm methane, but methane in the atmosphere is 1.9 ppm. Air above emission sites such as landfills, anaerobic digestor effluents, rice paddy effluents, and oil and gas wells contains elevated methane in the 500 ppm range. If such sites are targeted for methane removal, technology harnessing aerobic methanotroph metabolism has the potential to become economically and environmentally viable. The first step in developing such methane removal technology is to identify methanotrophs with enhanced ability to grow and consume methane at 500 ppm and lower. We report here that some existing methanotrophic strains grow well at 500 ppm methane, and one of them, Methylotuvimicrobium buryatense 5GB1C, consumes such low methane at enhanced rates compared to previously published values. Analyses of bioreactor-based performance and RNAseq-based transcriptomics suggest that this ability to utilize low methane is based at least in part on extremely low non-growth-associated maintenance energy and on high methane specific affinity. This bacterium is a candidate to develop technology for methane removal at emission sites. If appropriately scaled, such technology has the potential to slow global warming by 2050.

Specific affinity and relative abundance of methanogens in acclimated anaerobic sludge treating low-strength wastewater.

Kinetic parameters affecting effluent water quality including half saturation constant (Ks), maximum specific growth rate (µmax), and specific affinity ([Formula: see text], defined as µmax/Ks) were investigated using three types of anaerobic sludge (raw anaerobic digestion sludge referred to as unacclimated sludge, unacclimated sludge after endogenous decay, and sludge acclimated to low-strength wastewater in an anaerobic membrane bioreactor (AnMBR) for 360 days). Long-term acclimation to low-strength wastewater resulted in sludge with high specific affinity (1.6 × 10-3 L/mg COD/day for acclimated sludge compared to 4.1 × 10-4 L/mg COD/day for unacclimated sludge). The µmax values for unacclimated sludge and acclimated sludge were 0.08 and 0.07 day-1, respectively. The Ks values for unacclimated sludge and acclimated sludge were 194 ± 81 mg COD/L and 45 ± 13 mg COD/L, respectively. Although the Ks of unacclimated sludge after endogenous decay increased to 772 ± 74 mg COD/L, µmax increased to 0.35 day-1 as well, resulting in no statistically significant difference of [Formula: see text] between the two types of unacclimated sludge. Overall, [Formula: see text] is a better indicator than µmax or Ks alone for determining effluent water quality, as effluent substrate concentration is approximately inversely proportional to the specific affinity. 16S rRNA sequencing data analysis indicated a high abundance (85.8% of total archaea) of Methanosaeta in the microbial community after long-term acclimation. High [Formula: see text] associated with the enrichment of Methanosaeta appears to ensure successful anaerobic treatment of low-strength wastewater.

Affinity-binding immobilization of D-amino acid oxidase on mesoporous silica by a silica-specific peptide.

Enzyme immobilization is widely used for large-scale industrial applications. However, the weak absorption through physical methods limits the recovery ability. Here, affinity-binding immobilization of enzymes was explored using a silica-specific affinity peptide (SAP) as a fusion tag to intensify the binding force between the enzyme and mesoporous silica (MPS) carrier. D-amino acid oxidase (DAAO) of Rhodosporidium toruloides was used as a model enzyme. The optimal screened SAP (LPHWHPHSHLQP) was selected from a M13 phage display peptide library and fused to the C-terminal of DAAO to obtain fused DAAOs with one, two and three SAP tags, respectively. The activity of DAAO-SAP-MPS was superior comparing with DAAO-2SAP-MPS and DAAO-3SAP-MPS; meanwhile DAAO-SAP-MPS shows 36% higher activity than that of DAAO-MPS. Fusion with one SAP improved the thermal stability with a 10% activity increase for immobilized DAAO-SAP-MPS compared to that of DAAO-MPS at 50 °C for 3 h. Moreover, the activity recovery of immobilized DAAO-SAP-MPS was 25% higher in operation stability assessment after six-batch conversions of cephalosporin to glutaryl-7-amino cephalosporanic acid than that of DAAO-MPS.

Colorimetric determination of Hg(II) via the gold amalgam induced deaggregation of gold nanoparticles.

A method is described for the colorimetric determination of mercury(II). In the absence of Hg(II), aminopropyltriethoxysilane (APTES) which is positively charged at pH 7 is electrostatically absorbed on the surface of gold nanoparticles (AuNPs). This neutralizes the negative charges of the AuNPs and leads to NP aggregation and a color change from red to blue-purple. However, in the presence of Hg(II), reduced Hg (formed through the reaction between Hg(II) and citrate on the AuNP surface) will replace the APTES on the AuNPs. Hence, the formation of aggregates is suppressed and the color of the solution does not change. The assay is performed by measuring the ratio of absorbances at 650 and 520 nm and can detect Hg(II) at nanomolar levels with a 10 nM limit of detection. The specific affinity between mercury and gold warrants the excellent selectivity for Hg(II) over other environmentally relevant metal ions. Graphical Abstract Schematic of the method for determination of Hg2+ based on the gold amalgam-induced deaggregation of gold nanoparticles in the presence of APTES with the LOD of 10.1 nM.

Rapid separation of the low concentration Pd from Pd-Pt coexisting systems: Cyano-group's monomer-specific affinity.

Rapid separation of low concentration palladium (Pd) from Pd-Platinum (Pt) coexisting systems remains a formidable challenge, primarily due to the undifferentiated substitution of ligands in Pd/Pt complexes by adsorption sites. The development of an adsorbent featuring monomer-specific affinity adsorption sites for Pd/Pt could mitigate this drawback. Herein, Manganese hexacyanoferrate (MnHCF) possessing the sensitivity and specificity to Pd ions (Pd(II)) was synthesized via the facile co-precipitation method. MnHCF could rapidly and selectively capture 90.30 % of Pd(II) from a 10 ppm Pd-Pt coexisting system within just 5 min. Spectroscopic analyses and density functional theory (DFT) calculations indicated that cyano-group (CN) in MnHCF exhibited the monomer-specific affinity for targeted capturing Pd via the direct and strong coordination interaction (Fe-CN-PdCl2), which was co-determined by the electron-losing of C (0.06 e) and N (0.07 e) atom. At the same time, CN could neither react directly with the fully coordinated [PtCl6]2- species nor substitute the Cl- ligand, both of which contributed to the non-adsorption of Pt, thus triggering the Pd-Pt separation. This study provides a promising candidate adsorbent for practical applications in platinum group metals recovery by the design of adsorption sites with monomer-specific affinity.

Modifications of Ganoderma lucidum spores into digestive-tissue highly adherent porous carriers with selective affinity to hydrophilic or hydrophobic drugs.

Ganoderma lucidum spores (GLSs) have been suggested to provide optimal structures for transporting orally bioavailable drugs. However, the double-layer wall and cavities of GLSs are naturally closed. This study aimed to modify GLSs into porous carriers by opening the layers and internal cavity with iturin A (IA) followed by potassium hydroxide (KOH) or hydrochloric acid (HCl). The (IA + KOH)- and (IA + HCl)-treated GLS carriers exhibited a high loading rate of 301.50 ± 2.33 and 268.18 ± 7.72 mg/g for the hydrophilic methylene blue (MB) and hydrophobic rifampicin (RF), respectively. The mechanisms underlying the modification involved the enhancement of the specific surface area with IA and the exposure of hydrophilic groups or hydrophobic groups of the GLSs with KOH or HCl. The sustained 48-h molecule-release profiles of the MB- and RF-loaded GLS carriers were best fitted using a first-order kinetics model in simulated gastric (or intestinal) fluid compared with other models. In mice, the designed GLS carriers had high adhesion capacities onto the mucosa of the digestive tract and long retention times (120 h), and even promoted the secretion of mucus and expression of several key intestinal barrier proteins. This study provided a new method to modify GLSs into oral carriers with selective drug affinity, high loading capacity, sustained drug release, and high adhesion to the digestive tract.

Limited Mechanistic Link Between the Monod Equation and Methanogen Growth: a Perspective from Metabolic Modeling.

The Monod equation has been widely applied as the general rate law of microbial growth, but its applications are not always successful. By drawing on the frameworks of kinetic and stoichiometric metabolic models and metabolic control analysis, the modeling reported here simulated the growth kinetics of a methanogenic microorganism and illustrated that different enzymes and metabolites control growth rate to various extents and that their controls peak at either very low, intermediate, or very high substrate concentrations. In comparison, with a single term and two parameters, the Monod equation only approximately accounts for the controls of rate-determining enzymes and metabolites at very high and very low substrate concentrations, but neglects the enzymes and metabolites whose controls are most notable at intermediate concentrations. These findings support a limited link between the Monod equation and methanogen growth, and unify the competing views regarding enzyme roles in shaping growth kinetics. The results also preclude a mechanistic derivation of the Monod equation from methanogen metabolic networks and highlight a fundamental challenge in microbiology: single-term expressions may not be sufficient for accurate prediction of microbial growth. IMPORTANCE The Monod equation has been widely applied to predict the rate of microbial growth, but its application is not always successful. Using a novel metabolic modeling approach, we simulated the growth of a methanogen and uncovered a limited mechanistic link between the Monod equation and the methanogen's metabolic network. Specifically, the equation provides an approximation to the controls by rate-determining metabolites and enzymes at very low and very high substrate concentrations, but it is missing the remaining enzymes and metabolites whose controls are most notable at intermediate concentrations. These results support the Monod equation as a useful approximation of growth rates and highlight a fundamental challenge in microbial kinetics: single-term rate expressions may not be sufficient for accurate prediction of microbial growth.

Biomechanically, structurally and functionally meticulously tailored polycaprolactone/silk fibroin scaffold for meniscus regeneration.

Meniscus deficiency, the most common and refractory disease in human knee joints, often progresses to osteoarthritis (OA) due to abnormal biomechanical distribution and articular cartilage abrasion. However, due to its anisotropic spatial architecture, complex biomechanical microenvironment, and limited vascularity, meniscus repair remains a challenge for clinicians and researchers worldwide. In this study, we developed a 3D printing-based biomimetic and composite tissue-engineered meniscus scaffold consisting of polycaprolactone (PCL)/silk fibroin (SF) with extraordinary biomechanical properties and biocompatibility. We hypothesized that the meticulously tailored composite scaffold could enhance meniscus regeneration and cartilage protection. Methods: The physical property of the scaffold was characterized by scanning electron microscopy (SEM) observation, degradation test, frictional force of interface assessment, biomechanical testing, and fourier transform infrared (FTIR) spectroscopy analysis. To verify the biocompatibility of the scaffold, the viability, morphology, proliferation, differentiation, and extracellular matrix (ECM) production of synovium-derived mesenchymal stem cell (SMSC) on the scaffolds were assessed by LIVE/DEAD staining, alamarBlue assay, ELISA analysis, and qRT-PCR. The recruitment ability of SMSC was tested by dual labeling with CD29 and CD90 by confocal microscope at 1 week after implantation. The functionalized hybrid scaffold was then implanted into the meniscus defects on rabbit knee joint for meniscus regeneration, comparing with the Blank group (no scaffold) and PS group. The regenerated meniscus tissue was evaluated by histological and immunohistochemistry staining, and biomechanical test. Macroscopic and histological scoring was performed to assess the outcome of meniscus regeneration and cartilage protection in vivo. Results: The combination of SF and PCL could greatly balance the biomechanical properties and degradation rate to match the native meniscus. SF sponge, characterized by fine elasticity and low interfacial shear force, enhanced energy absorption capacity of the meniscus and improved chondroprotection. The SMSC-specific affinity peptide (LTHPRWP; L7) was conjugated to the scaffold to further increase the recruitment and retention of endogenous SMSCs. This meticulously tailored scaffold displayed superior biomechanics, structure, and function, creating a favorable microenvironment for SMSC proliferation, differentiation, and extracellular matrix (ECM) production. After 24 weeks of implantation, the histological assessment, biochemical contents, and biomechanical properties demonstrated that the polycaprolactone/silk fibroin-L7 (PS-L7) group was close to the native meniscus group, showing significantly better cartilage protection than the PS group. Conclusion: This tissue engineering scaffold could greatly strengthen meniscus regeneration and chondroprotection. Compared with traditional cell-based therapies, the meniscus tissue engineering approach with advantages of one-step operation and reduced cost has a promising potential for future clinical and translational studies.

Impact of decreasing hydraulic retention times on the specific affinity of methanogens and their community structures in an anaerobic membrane bioreactor process treating low strength wastewater.

Maximum specific growth rate (µmax) and substrate saturation constant (Ks) are widely used in determining the growth of microorganisms. The ratio (µmax/Ks), also referred to as specific affinity, aA0, is a better parameter to assess the advantage in competition for substrates by bridging microbial growth and the kinetics of enzymatic substrate uptake, but is not well studied. This study investigated the effect of hydraulic retention time (HRT) on the aA0 of anaerobic sludge from an anaerobic membrane bioreactor (AnMBR), associated microbial communities and the overall wastewater treatment performance. The AnMBR was fed with acetate wastewater (~500 mg COD/L) and operated at fixed solids retention time (45 d) while HRT continued to decrease. There was no significant difference in Ks (ranging from 170 to 243 mg COD/L) at different HRTs. However, aA0 increased from (4.0 ± 0.2) × 10-4 to (4.9 ± 0.2) × 10-4 and to (6.5 ± 0.1) × 10-4 L/mg COD/d as HRT decreased from 24 h to 12 h and further to 6 h, respectively. This was accompanied by the increase in acetoclastic methanogens (mainly Methanosaeta) from 3.85 × 1010, 8.82 × 1010 to 1.05 × 1011 cells/L, respectively. The fraction of Methanosaeta in the anaerobic biomass increased from 33.67% to 61.08% as HRT decreased from 24 h to 6 h. Correspondingly, effluent quality was improved, as evidenced from the COD concentrations of 32 ± 6, 21 ± 4, and 13 ± 5 mg/L at the HRTs of 24 h, 12 h, and 6 h, respectively. The results confirm that microorganisms are able to adapt to growth conditions by adjusting their kinetic properties and suggest that short HRTs in the AnMBR favor the growth and accumulation of Methanosaeta with high specific affinity likely because they can compete for acetate at low concentrations by increasing substrate uptake rate and thus specific microbial growth rate.

E7 peptide-functionalized Ti6Al4V alloy for BMSC enrichment in bone tissue engineering.

Ti6Al4V alloy is widely used for hip joint prostheses, however owing to its lack of biomimetic surface properties, it often suffers from poor osseointegration. It is well known that bone mesenchymal stem cells (BMSCs) play an important role in the osseointegration of the host bone and joint prostheses. One promising approach to improving the osseointegration of joint prostheses is to enrich the number of BMSCs at the periprosthetic site. Previous studies have reported that BMSC specific affinity peptide E7, can specifically enrich BMSCs. However, to date, few studies have reported the use of E7 in bone tissue engineering. In this study, we conjugated E7 peptide to Ti6Al4V alloy to fabricate a scaffold (BTS) to improve the biocompatibility of the alloy. E7 peptide efficiently improved the adhesion of BMSCs to Ti6Al4V alloy. In addition, the BTS scaffold was more conducive to osteogenesis than the RGD-functionalized and non-functionalized control scaffolds. The functional BTS scaffold could pave the way for designing functional joint prostheses, which promote osseointegration between the host bone and implant.

Ultrastrong and Bioactive Nanostructured Bio-Based Composites.

Nature's design of functional materials relies on smart combinations of simple components to achieve desired properties. Silk and cellulose are two clever examples from nature-spider silk being tough due to high extensibility, whereas cellulose possesses unparalleled strength and stiffness among natural materials. Unfortunately, silk proteins cannot be obtained in large quantities from spiders, and recombinant production processes are so far rather expensive. We have therefore combined small amounts of functionalized recombinant spider silk proteins with the most abundant structural component on Earth (cellulose nanofibrils (CNFs)) to fabricate isotropic as well as anisotropic hierarchical structures. Our approach for the fabrication of bio-based anisotropic fibers results in previously unreached but highly desirable mechanical performance with a stiffness of ∼55 GPa, strength at break of ∼1015 MPa, and toughness of ∼55 MJ m-3. We also show that addition of small amounts of silk fusion proteins to CNF results in materials with advanced biofunctionalities, which cannot be anticipated for the wood-based CNF alone. These findings suggest that bio-based materials provide abundant opportunities to design composites with high strength and functionalities and bring down our dependence on fossil-based resources.

Biodegradation kinetics of toluene, m-xylene, p-xylene and their intermediates through the upper TOL pathway in Pseudomonas putida (pWWO).

Pseudomonas putida mt-2, harbouring TOL plasmid pWWO, is capable of degrading toluene and a range of di- and tri-alkylbenzenes. In this study, chemostat-grown cells (D = 0.05 h-1, toluene or m-xylene limitation) of this strain were used to assess the kinetics of the degradation of toluene, m-xylene, p-xylene, and a number of their pathway intermediates. The conversion kinetics for the three hydrocarbons showed significant differences: the maximal conversion rates were rather similar [11-14 mmol h-1 (g dry wt)-1] but the specific affinity (the slope of the v vs s curve near the origin) of the cells for toluene [1300 I (g dry wt)-1 h-1] was only 5% and 14% of those found for m-xylene and p-xylene, respectively. Consumption kinetics of mixtures of the hydrocarbons confirmed that xylenes are strongly preferred over toluene at low substrate concentrations. The maximum flux rates of pathway intermediates through the various steps of the TOL pathway as far as ring cleavage were also determined. Supply of 0-5 mM 3-methylbenzyl alcohol or 3-methylbenzaidehyde to fully induced cells led to the transient accumulation of 3-methylbenzoate. Accumulation of the corresponding carboxylic acid (benzoate) was also observed after pulses of benzyl alcohol and benzaldehyde, which are intermediates in toluene catabolism. Analysis of consumption and accumulation rates for the various intermediates showed that the maximal rates at which the initial monooxygenation step and the conversion of the carboxylic acids by toluate 1,2-dioxygenase may occur are two- to threefold lower than those measured for the two intermediate dehydrogenation steps.

Fluorous affinity-based separation techniques for the analysis of biogenic and related molecules.

Perfluoroalkyl-containing compounds have a unique 'fluorous' property that refers to the remarkably specific affinity they share. Fluorous compounds can be easily isolated from non-fluorous species on the perfluoroalkyl-functionalized stationary phases used in fluorous solid-phase extraction and fluorous liquid chromatography by means of fluorous-fluorous interactions (fluorophilicity). Recently, this unique specificity has been applied to the highly selective enrichment and analysis of different classes of biogenic and related compounds in complex samples. Because the biogenic compounds are generally not 'fluorous', they must be derivatized with appropriate perfluoroalkyl group-containing reagent in order to utilize fluorous interaction. In this review, we introduce the application of fluorous affinity techniques including derivatization methods to biogenic sample analysis.