External Substrates Research Articles

13C-Labelled Glucose Reveals Shifts in Fermentation Pathway During Cathodic Electro-Fermentation with Mixed Microbial Culture.

Cathodic Electro-Fermentation (CEF) is an innovative approach to manage the spectrum of products deriving from anaerobic fermentation. Herein, mixed microbial culture fermentation using a ternary mixture containing labelled 13C glucose and non-labelled acetate and ethanol was studied to identify the role of polarization on the metabolic pathways of glucose fermentation. CEF at an applied potential of -700 mV (vs. SHE, Standard Hydrogen Electrode) enhanced the production yield of acetate, propionate, and butyrate (0.90±0.10, 0.22±0.03, and 0.34±0.05 mol/mol; respectively) compared to control tests performed at open circuit potential (OCP) (0.54±0.09, 0.15±0.04, and 0.20±0.001 mol/mol, respectively). Results indicate that CEF affected the 13C labelled fermented product levels and their fractional 13C enrichments, allowing to establish metabolic pathway models. This work demonstrates that, under cathodic polarization, the abundance of both fully 13C labelled propionate and butyrate isotopomers increased compared to control tests. The effect of CEF is mainly due to intermediates initially produced from the glucose metabolic transformation in the presence of non-labelled acetate and ethanol as external substrates. These findings represent a significant advancement in current knowledge of CEF, which offers a promising tool to control mixed cultures bioprocesses.

Self-stacked small molecules for ultrasensitive, substrate-free Raman imaging in vivo.

Raman spectroscopy using surface-enhanced Raman scattering (SERS) nanoprobes represents an ultrasensitive and high-precision technique for in vivo imaging. Clinical translation of SERS nanoprobes has been hampered by biosafety concerns about the metal substrates used to enhance Raman signals. We report a set of small molecules with bis-thienyl-substituted benzobisthiadiazole structures that enhance Raman signal through self-stacking rather than external substrates. In our technique, called stacking-induced charge transfer-enhanced Raman scattering (SICTERS), the self-stacked small molecules form an ordered spatial arrangement that enables three-dimensional charge transfer between neighboring molecules. The Raman scattering cross-section of SICTERS nanoprobes is 1350 times higher than that of conventional SERS gold nanoprobes of similar particle size. SICTERS outperforms SERS in terms of in vivo imaging sensitivity, resolution and depth. SICTERS is capable of noninvasive Raman imaging of blood and lymphatic vasculatures, which has not been achieved by SERS. SICTERS represents an alternative technique to enhance Raman scattering for guiding the design of ultrasensitive substrate-free Raman imaging probes.

IMSIS: An instrumented microphysiological system with integrated sensors for monitoring cellular metabolic activities

Well plates are widely used in biological experiments, particularly in pharmaceutical sciences and cell biology. Its popularity stems from its versatility to support a variety of fluorescent markers for high throughput monitoring of cellular activities. However, using fluorescent markers in traditional well plates has its own challenges, namely, they can be potentially toxic to cells, and thus, may perturb their biological functions; and it is difficult to monitor multiple analytes concurrently and in real-time inside each well. This paper presents a fully instrumented microphysiological system with integrated sensors (IMSIS) with a similar well format. Each well in the microphysiological system has a set of sensors for monitoring multiple metabolic analytes in real-time. The IMSIS platform is supported by integrated bioelectronic circuits and a graphical user interface for easy user configuration and monitoring. The system has integrated microfluidics to maintain its microphysiological environment within each well. The IMSIS platform currently incorporates O2, H2O2, and pH sensors inside each well, allowing up to six wells to perform concurrent measurements in real-time. Furthermore, the architecture is scalable to achieve an even higher level of throughput. The miniaturized design ensures portability, suitable for small offices and field applications.The IMSIS platform was successfully used to monitor in real-time the mitochondrial functions of live bovine embryos in O2 consumption, H2O2 release as an indication of ROS production, and extracellular acidity changes before and after the introduction of external substrates.

Bioproduction of exopolysaccharides by lactic acid bacteria using agave by-products

The capacity to produce exopolysaccharides (EPS) is well known among several microorganisms, especially lactic acid bacteria (LAB). However, the physiological role of these polymers has yet to be elucidated. Nevertheless, it has been observed that LAB growth conditions and adaptation to external environments and substrates are directly related to EPS biosynthesis. This study aimed to evaluate alternative carbon sources from agave by-products to synthesize EPS with LAB. Native LAB from the genera Lactococcus and Lactiplantibacillus were evaluated for their ability to produce EPS from simple carbon sources; they showed potential to produce EPS, presenting positive results on Congo red plates using glucose and fructose as carbon sources. In addition, native LAB could synthesize EPS from agave leaves and bagasse. L. plantarum ITD-ZC-107 stand out in the production of EPS, especially from bagasse. Thermostability of EPS from the evaluated carbon sources was analyzed. EPS from agave leaves and bagasse showed a higher degradation temperature than the ones obtained from glucose and sucrose, indicating better thermo-resistance.

New insight into Na+-promoted microbial electrolysis cell towards hydrogen energy recovery: Feasibility and dual mechanism in salt-containing wastewater treatment

The salt-containing wastewater treatment has become serious challenge, while conductivity and micro-ecosystem disorder severely limited microbial electrolysis cell (MEC) efficiency. In order to synchronously overcome the above bottlenecks, this study proposed an innovative Na+-promoted MEC system for efficient salt-containing wastewater treatment. The Na+ presence greatly improved conductivity to impair electric resistance, resulting in rapid electron transfer pattern towards organic degradation in anode and hydrogen synthesis in cathode. Furthermore, the selective Na+ stress triggered microbial community evolution and improved electroactive bacteria activity after salinity cultivation in MEC (0.09–0.17 mol Na+/L), which played “bacteria screening” role for salt-tolerant “electrochemical hydrogen-producing” bacteria community formation. The organic-degrading and hydrogen-producing bacteria with their assistors were tolerant to Na+ stress, which were considerably enriched into dominant microorganisms, while the unfavorable bacteria responsible for hydrogen consumption and competition were inhibited due to salinity-sensitivity. Correspondingly, the metabolic pathways for metabolism, genetic information processing and environmental information processing were improved, positively associating with organic degradation and hydrogen production. Such dual driving contributions of Na+-improved electron transfer-utilization pattern and Na+-modified microbial metabolisms boosted the organic pollutant degradation at anode to 91.34 % while improving the performance and speeds of hydrogen production by 1.57–1.70 times. The hydrogen abundance was also increased to 71.57 % in biogas. The energy efficiencies relative to external electricity and substrates were elevated by 8.80–28.44 %, the coulombic efficiency raised by 14.05 % and reached 109.72 %, suggesting the positive net energy benefits. The findings provided inspirations to the feasible application of MEC in salt-containing wastewater treatment with efficiency benefits.

Synthesis, characterization and reactivity of a Mn(III)–hydroxido complex as a biomimetic model for lipoxygenase

Manganese hydroxido (Mn–OH) complexes supported by a tripodal N,N′,N″-[nitrilotris(ethane-2,1-diyl)]tris(P,P-diphenylphosphinic amido) ([poat]3−) ligand have been synthesized and characterized by spectroscopic techniques including UV–vis and electron paramagnetic resonance (EPR) spectroscopies. X-ray diffraction (XRD) methods were used to confirm the solid-state molecular structures of {Na2[MnIIpoat(OH)]}2 and {Na[MnIIIpoat(OH)]}2 as clusters that are linked by the electrostatic interactions between the sodium counterions and the oxygen atom of the ligated hydroxido unit and the phosphinic (P=O) amide groups of [poat]3−. Both clusters feature two independent monoanionic fragments in which each contains a trigonal bipyramidal Mn center that is comprised of three equatorial deprotonated amide nitrogen atoms, an apical tertiary amine, and an axial hydroxido ligand. XRD analyses of {Na[MnIIIpoat(OH)]}2 also showed an intramolecular hydrogen bonding interaction between the MnIII–OH unit and P=O group of [poat]3−. Crystalline {Na[MnIIIpoat(OH)]}2 remains as clusters with Na+---O interactions in solution and is unreactive toward external substrates. However, conductivity studies indicated that [MnIIIpoat(OH)]− generated in situ is monomeric and reactivity studies found that it is capable of cleaving C-H bonds, illustrating the importance of solution-phase speciation and its direct effect on chemical reactivity.Synopsis: Manganese–hydroxido complexes were synthesized to study the influence of H-bonds in the secondary coordination sphere and their effects on the oxidative cleavage of substrates containing C-H bonds.

Interpreting the differences in microbial carbon and nitrogen use efficiencies estimated by 18O labeling and ecoenzyme stoichiometry

Microbial carbon and nitrogen use efficiencies (CUE and NUE) are central to our understanding of soil C and N cycling. Although both the 18O-labeling approach and ecoenzyme stoichiometry model have been widely used to estimate microbial CUE and NUE, comparisons of the two methods are scarce. Here, we investigated soil microbial CUE and NUE of 11 locations along a forest transect in eastern China using both the 18O-approach and ecoenzyme model. We found that microbial CUE-18O and NUE-18O estimated by the 18O-approach were positively related to each other and both decreased with soil acidification and phosphorus acquisition as measured by enzyme activity. However, CUEC:N and NUEN:C, estimated by C:N stoichiometry using the enzyme model were negatively related to each other and neither showed any relationship to soil acidification or phosphorus acquisition. Finally, CUEC:P and NUEN:P estimated according to C:P stoichiometry were positively related to each other and both increased with soil acidification and phosphorus acquisition efforts. We suggest that a reason for these differences is that the 18O-approach reflects the intracellular biochemical transformation of C, N, and P while the enzyme models reflect stoichiometric imbalances between external substrates and microbial biomass, i.e., different aspects of microbial metabolism. Moreover, differences between the C:N and C:P-based enzyme models resulted from P-limitation to soil microorganisms in this system. For these reasons, microbial element use efficiencies need to be clearly defined, i.e., as derived from growth-based or soil enzyme-based measurements, and caution must be made when comparing results obtained from different methods, and under different conditions of resource availability.

PON1 has palmitoyl-protein thioesterase (PPT) activity, and can affect the presence of SR-B1 on the endothelial cell membrane.

The high-density lipoprotein (HDL)-associated enzyme paraoxonase 1 (PON1) is expressed almost exclusively in the liver and is then transported by HDL to the peripheral tissues. The lipophilic nature of PON1 enables its easy exchange between the lipoprotein and cell membranes in a process that is dependent on the HDL receptor scavenger receptor class B, type 1 (SR-B1). In endothelial cells, PON1 binding to the cell membrane leads to its internalization by endocytosis and subsequent lysosomal degradation. PON1 is a "promiscuous" enzyme with unusually broad substrate specificity in vitro, but its actual function and substrate are still unknown. The enzyme requires a lipid environment and becomes completely inactive upon delipidation. However, when PON1 binds HDL, its active site faces the lipoprotein's core and is inaccessible to external substrates. Hence, the HDL-bound PON1 is inactive toward substrates outside the particle's lipid core and is rapidly degraded and becomes inactive upon internalization. Consequently, the enzyme is only active in the cell membrane during its transit from HDL to the cytoplasm. To assign a function to PON1, we investigated whether it is a palmitoyl-protein thioesterase (PPT) that can hydrolyze the palmitoyl moieties of membrane proteins involved in HDL and cholesterol transport, such as SR-B1, ABCA1, or their neighboring caveola proteins to facilitate the release of HDL or trigger its endocytosis. This study shows that PON1 can hydrolyze palmitoyl-cysteine thioester bonds in vitro, has direct or indirect PPT activity in vivo, and can significantly decrease the presence of SR-B1 in the endothelial membrane.

Cellular RNA levels define heterotrophic substrate-uptake rate sub-guilds in activated sludge microbial communities.

A heterotrophic-specialist model was proposed previously to divide wastewater treatment plant (WWTP) heterotrophs into sub-guilds of consumers of readily or slowly degradable substrates (RDS or SDS, respectively). The substrate degradation rate model coupled to metabolic considerations predicted that RNA and polyhydroxyalkanoate (PHA) levels would be positively correlated in the activated sludge communities with high RNA and PHA occurring in RDS-consumers, and low RNA with no PHA accumulation occurring in SDS-consumers because their external substrates are always present. This prediction was verified in previous studies and in the current one. Thus, RNA and PHA levels were used as biomarkers of the RDS- and SDS-consumer sub-guilds for cell sorting using flow cytometry of samples from three WWTPs. Subsequently, 16S rRNA gene amplicon sequencing revealed that the sorted groups were highly similar over time and among WWTPs, and demonstrated a clear segregation by RNA levels. Predicted ecophysiological traits based on 16S rRNA phylogeny suggested that the high-RNA population showed RDS-consumer traits such as higher rrn copy numbers per genome. Using a mass-flow immigration model, it appeared that the high-RNA populations exhibited high immigration rates more frequently than low-RNA populations, but the differences in frequencies were less with increasing solids residence times.

Oxygen transfer reactivity mediated by nickel perfluoroalkyl complexes using molecular oxygen as a terminal oxidant.

Nickel perfluoroethyl and perfluoropropyl complexes supported by naphthyridine-type ligands show drastically different aerobic reactivity from their trifluoromethyl analogs resulting in facile oxygen transfer to perfluoroalkyl groups or oxygenation of external organic substrates (phosphines, sulfides, alkenes and alcohols) using O2 or air as a terminal oxidant. Such mild aerobic oxygenation occurs through the formation of spectroscopically detected transient high-valent NiIII and structurally characterized mixed-valent NiII-NiIV intermediates and radical intermediates, resembling O2 activation reported for some Pd dialkyl complexes. This reactivity is in contrast with the aerobic oxidation of naphthyridine-based Ni(CF3)2 complexes resulting in the formation of a stable NiIII product, which is attributed to the effect of greater steric congestion imposed by longer perfluoroalkyl chains.

Fe(II) complexes of pyridine-substituted thiosemicarbazone ligands as catalysts for oxidations with hydrogen peroxide.

The reaction of three [FeII(TSC)2] complexes, where TSC is a pyridine-substituted thiosemicarbazone of the HDpT or HBpT families, with H2O2 in acetonitrile solution does not result in the accumulation of the corresponding [FeIII(TSC)2]+ complexes. Instead, a mixture of diamagnetic low-spin FeII species is generated. According to the MS spectra, those species result from the sequential addition of up to five oxygen atoms to the complex. This capability for the addition of oxygen atoms suggested that oxygen atom transfer to external substrates may be possible, and these TSC complexes were tested in the oxidation of thioanisole and styrene with H2O2. As hypothesized, the complexes are active in both the oxidation of thioanisole to its sulfoxide and styrene to benzaldehyde, with time scales indicating the participation of the species containing added oxygen atoms. Interestingly, the free thiosemicarbazone ligands and the [Zn(Dp44mT)2] complex also catalyse the selective sulfoxidation of thioanisole, but they are ineffective in catalysing styrene oxidation to benzaldehyde. These findings open up new directions for the development of thiosemicarbazone-based metal catalysts for oxidation processes.

Effects of organic substrates on sulfate-reducing microcosms treating acid mine drainage: Performance dynamics and microbial community comparison

Bioremediation techniques utilizing sulfate-reducing bacteria (SRB) for acid mine drainage (AMD) treatment have attracted growing attention in recent years, yet substrate bioavailability for SRB is a key factor influencing treatment effectiveness and long-term stability. This study investigated the effects of external organic substrates, including four complex organic wastes (i.e., sugarcane bagasse, straw compost, shrimp shell (SS), and crab shell (CS)) and a small-molecule organic acid (i.e., propionate), on AMD removal performance and associated microbial communities during the 30-day operation of sulfate-reducing microcosms. The results showed that the pH values increased in all five microcosms, while CS exhibited the highest neutralization ability and a maximum alkalinity generation of 1507 mg/L (as CaCO3). Sulfate reduction was more effective in SS and CS microcosms, with sulfate removal efficiencies of 95.6% and 86.0%, respectively. All sulfate-reducing microcosms could remove heavy metals to different degrees, with the highest removal rate of >99.0% observed for aluminum. The removal efficiency of manganese, the most recalcitrant metal, was the highest (96%) in the CS microcosm. Correspondingly, SRB was more abundant in the CS and SS microcosms as revealed by sequencing analysis, while Desulfotomaculum was the dominant SRB in the CS microcosm, accounting for 10.8% of total effective bacterial sequences. Higher abundances of functional genes involved in fermentation and sulfur cycle were identified in CS and SS microcosms. This study suggests that complex organic wastes such as CS and SS could create and maintain preferable micro-environments for active growth and metabolism of functional microorganisms, thus offering a cost-efficient, stable, and environmental-friendly solution for AMD treatment and management.

Geometric trade-off between contractile force and viscous drag determines the actomyosin-based motility of a cell-sized droplet

Cell migration in confined environments is fundamental for diverse biological processes from cancer invasion to leukocyte trafficking. The cell body is propelled by the contractile force of actomyosin networks transmitted from the cell membrane to the external substrates. However, physical determinants of actomyosin-based migration capacity in confined environments are not fully understood. Here, we develop an in vitro migratory cell model, where cytoplasmic actomyosin networks are encapsulated into droplets surrounded by a lipid monolayer membrane. We find that the droplet can move when the actomyosin networks are bound to the membrane, in which the physical interaction between the contracting actomyosin networks and the membrane generates a propulsive force. The droplet moves faster when it has a larger contact area with the substrates, while narrower confinement reduces the migration speed. By combining experimental observations and active gel theory, we propose a mechanism where the balance between sliding friction force, which is a reaction force of the contractile force, and viscous drag determines the migration speed, providing a physical basis of actomyosin-based motility in confined environments.

Structure and Reactivity of Nonporphyrinic Terminal Manganese(IV)–Hydroxide Complexes in the Oxidative Electrophilic Reaction

High-valent transition metal-hydroxide complexes have been proposed as essential intermediates in biological and synthetic catalytic reactions. In this work, we report the single-crystal X-ray structure and spectroscopic characteristics of a mononuclear nonporphyrinic MnIV-(OH) complex, [MnIV(Me3-TPADP)(OH)(OCH2CH3)]2+ (2), using various physicochemical methods. Likewise, [MnIV(Me3-TPADP)(OH)(OCH2CF3)]2+ (3), which is thermally stable at room temperature, was also synthesized and characterized spectroscopically. The MnIV-(OH) adducts are capable of performing oxidation reactions with external organic substrates such as C-H bond activation, sulfoxidation, and epoxidation. Kinetic studies, involving the Hammett correlation and kinetic isotope effect, and product analyses indicate that 2 and 3 exhibit electrophilic oxidative reactivity toward hydrocarbons. Density functional theory calculations support the assigned electronic structure and show that direct C-H bond activation of the MnIV-(OH) species is indeed possible.

Copper Mediated Intramolecular vs. Intermolecular Oxygenations: The Spacer makes the Difference!

AbstractCopper complexes in combination with dioxygen are important as potential catalytic systems for regio‐ and stereoselective aerobic oxygenations of aromatic and aliphatic C−H bonds at ambient temperatures. In that context we herein describe a copper(I) complex with an imine ligand derived from (+)‐camphor and 2‐(2‐aminoethyl)pyridine that forms a bis(μ‐hydroxido) dicopper complex upon reaction with dioxygen at room temperature. It is detectable by UV‐vis for several hours up to a few days, depending on the solvent and could be structurally characterized. In contrast to previous observations this complex rather oxygenates acetone or thioanisole as external substrates instead of undergoing an intramolecular ligand hydroxylation.

Organic Matter Degradation in Energy-Limited Subsurface Environments—A Bioenergetics-Informed Modeling Approach

Microbial degradation of organic matter is a key driver of subsurface biogeochemistry. Here, we present a bioenergetics-informed kinetic model for the anaerobic degradation of macromolecular organic matter that accounts for extracellular hydrolysis, fermentation, and respiration. The catabolic energy generated by fermentation and respiration is allocated to biomass growth, production of extracellular hydrolytic enzymes, and cellular maintenance. Microbial cells are assumed to exist in active or dormant states with marked differences in maintenance energy requirements. Dormant cells are further assumed to fulfill their maintenance energy requirements by utilizing their own biomass instead of relying on external substrates. When the catabolic Gibbs energy production for a given functional group of microorganisms exceeds the total maintenance energy requirement of the active cells, biomass growth, re-activation of dormant cells, and production of extracellular hydrolytic enzymes are possible. The latter, in turn, allows the microbial community to access more of the available external organic substrates. In the opposite case, active cells decay or become dormant. We apply the model to simulate the anaerobic degradation of cellulose by a hypothetical microbial community consisting of cellulolytic fermenting bacteria and sulfate-reducing bacteria, under conditions representative of those encountered in water-saturated subsurface environments.

Semiempirical method for examining asynchronicity in metal–oxido-mediated C–H bond activation

The oxidation of substrates via the cleavage of thermodynamically strong C-H bonds is an essential part of mammalian metabolism. These reactions are predominantly carried out by enzymes that produce high-valent metal-oxido species, which are directly responsible for cleaving the C-H bonds. While much is known about the identity of these transient intermediates, the mechanistic factors that enable metal-oxido species to accomplish such difficult reactions are still incomplete. For synthetic metal-oxido species, C-H bond cleavage is often mechanistically described as synchronous, proton-coupled electron transfer (PCET). However, data have emerged that suggest that the basicity of the M-oxido unit is the key determinant in achieving enzymatic function, thus requiring alternative mechanisms whereby proton transfer (PT) has a more dominant role than electron transfer (ET). To bridge this knowledge gap, the reactivity of a monomeric MnIV-oxido complex with a series of external substrates was studied, resulting in a spread of over 104 in their second-order rate constants that tracked with the acidity of the C-H bonds. Mechanisms that included either synchronous PCET or rate-limiting PT, followed by ET, did not explain our results, which led to a proposed PCET mechanism with asynchronous transition states that are dominated by PT. To support this premise, we report a semiempirical free energy analysis that can predict the relative contributions of PT and ET for a given set of substrates. These findings underscore why the basicity of M-oxido units needs to be considered in C-H functionalization.

Dioxygen Activation and Pyrrole α-Cleavage with Calix[4]pyrrolato Aluminates: Enzyme Model by Structural Constraint.

The present work describes the reaction of triplet dioxygen with the porphyrinogenic calix[4]pyrrolato aluminates to alkylperoxido aluminates in high selectivity. Multiconfigurational quantum chemical computations disclose the mechanism for this spin‐forbidden process. Despite a negligible spin–orbit coupling constant, the intersystem crossing (ISC) is facilitated by singlet and triplet state degeneracy and spin–vibronic coupling. The formed peroxides are stable toward external substrates but undergo an unprecedented oxidative pyrrole α‐cleavage by ligand aromatization/dearomatization‐initiated O−O σ‐bond scission. A detailed comparison of the calix[4]pyrrolato aluminates with dioxygen‐related enzymology provides insights into the ISC of metal‐ or cofactor‐free enzymes. It substantiates the importance of structural constraint and element–ligand cooperativity for the functions of aerobic life.

Isomerization Reactions in Anionic Mesoionic Carbene-Borates and Control of Properties and Reactivities in the Resulting CoII Complexes through Agostic Interactions.

We present herein anionic borate‐based bi‐mesoionic carbene compounds of the 1,2,3‐triazol‐4‐ylidene type that undergo C−N isomerization reactions. The isomerized compounds are excellent ligands for CoII centers. Strong agostic interactions with the “C−H”‐groups of the cyclohexyl substituents result in an unusual low‐spin square planar CoII complex, which is unreactive towards external substrates. Such agostic interactions are absent in the complex with phenyl substituents on the borate backbone. This complex displays a high‐spin tetrahedral CoII center, which is reactive towards external substrates including dioxygen. To the best of our knowledge, this is also the first investigation of agostic interactions through single‐crystal EPR spectroscopy. We conclusively show here that the structure and properties of these CoII complexes can be strongly influenced through interactions in the secondary coordination sphere. Additionally, we unravel a unique ligand rearrangement for these classes of anionic mesoionic carbene‐based ligands.

A tactile sensor for simultaneous measurements of 6-axis force/torque and the coefficient of static friction

We propose a new design for a tactile sensor that simultaneously measures 6-axis force/torque and the coefficient of static friction, which will enable robotic fingers to handle a slippery object while preventing both translational and rotational slips. The sensor consists of internal and external substrates, internal and external elastomers and normal/shear stress sensor chips. The sensor chips are arranged on the substrates and embedded in the elastomers to measure the deformation of the elastomers. The coefficient of static friction is estimated from the normal and spread deformations of the external elastomer. The 6-axis force/torque values are estimated from the normal, shear and torsional deformations of the internal elastomer. We evaluated the sensor responses when the sensor came into contact with various objects with different coefficients of static friction. We confirmed that the coefficient of static friction and the 6-axis force/torque changes were able to be estimated from the sensor outputs.