Gut flora metagenomic analysis coupled with metabolic and deep immune profiling in chronic kidney disease

BACKGROUND AND HYPOTHESIS

Perturbation of gut microbiota has been linked to chronic kidney disease (CKD), which was correlated with a sophisticated milieu of metabolic and immune dysregulation.

METHODS

To clarify the underlying host-microbe interaction in CKD, we performed multi-omics measurements, including systems-level gut microbiome, targeted serum metabolome, and deep immunotyping, in a cohort of patients and non-CKD controls.

RESULTS

Our analyses on functional profiles of gut microbiome showed a decrease in the diversity and abundance of carbohydrate-active enzyme (CAZyme) genes but an increase in the abundance of antibiotic resistance, nitrogen cycling enzyme, and virulence factor genes in CKD. Moreover, models generated using measurements of serum metabolites (amino acids, bile acids, and short-chain fatty acids) or immunotypes were predictive of renal impairment but less so than many of functional profiles derived from gut microbiota, with the CAZyme genes being the top performing model to accurately predict early stage of diseases. In addition, co-occurrence analyses revealed coordinated host-microbe relationships in CKD. Specifically, the highest fractions of significant correlations were identified with circulating metabolites by several taxonomic and functional profiles of gut microbiome, while immunotype features were moderately associated with the abundance of microbiome-encoded metabolic pathways and serum levels of amino acids (e.g. B cell cluster-tryptophan and B cell cluster-tryptophan metabolism).

CONCLUSION

Overall, our multi-omics integration revealed several signatures of systems-level gut microbiome in robust associations with host-microbe co-metabolites and renal function, which may be of etiological and diagnostic implications in CKD.

Photodissociation Dynamics of CO-Forming Channels on the Ground-State Surface of Methyl Formate at 248 nm: Direct Dynamics Study and Assessment of Generalized Multicenter Impulsive Models

The photodissociation dynamics of methyl formate in the electronic ground state S₀, initiated by a 248 nm-wavelength laser, is studied by direct dynamics simulations. We analyze five channels, where four of them have as products CH₃OH + CO, one leading to the formation of three fragments, H₂CO + H₂ + CO, and a channel characterized by a roaming transition state. The analysis of energy distribution among the degrees of freedom of the product and the comparison with experimental results previously published by other groups provide the ingredients to distinguish the examined dissociation pathways. The interpretation of the results proves that the characterization of dissociation mechanisms must rely on a dynamics approach involving multiple electronic states, including considerations on the features of the S₁/S₀ conical intersection. Here, we also assess the generalized multicenter impulsive model, GMCIM, that has been designed for dissociation processes with exit barriers, and the energy distribution in the products is predicted on the basis of information from the saddle points and the intrinsic reaction coordinates. Main features, advantages, limits, and future perspectives of the method are reported and discussed.

Vectorial imaging of the photodissociation of 2-bromobutane oriented via hexapolar state selection

Molecular orientation techniques are becoming available in the study of elementary chemical processes, in order to highlight those structural and dynamical properties that would be concealed by random rotational motions. Recently successful orientation was achieved for asymmetric-top and chiral molecules of much larger complexity than hitherto. In this work, we report and discuss the correlation between the vectors' photofragment recoil velocity v, transition dipole moment μ, and permanent dipole moment d in a dissociation experiment on hexapole oriented 2-bromobutane, photoinitiated by a linearly polarized laser. The sliced ion images of the Br*(2P1/2) and Br(2P3/2) photofragments were acquired at 234.0 and 254.1 nm, respectively, by a (2 + 1) resonance-enhanced multiphoton ionization technique. A detailed analysis of the sliced ion images obtained at a tilting angle 45° of laser polarization provides information on the correlation of the three vectors, which are confined by two polar angles α and χ and one azimuthal angle φμd in the recoil frame. The sliced ion images of Br fragments eliminated individually from the enantiomers at 254.1 nm yield an asymmetric factor close to zero; for this reason the photofragment angular distributions do not show significant differences. The elimination of the Br* fragment at 234.0 nm is mainly correlated with a parallel transition, giving rise to a large anisotropy parameter of 1.85, and thus can be considered as a single state excitation. The resulting recoil frame angles are optimized to 163° ± 8° and 164° ± 1° for α and χ, respectively, whereas φμd is approaching 0° for the best fit. Since for the present molecule, the three vectors have an only slight spatial arrangement, the photofragment angular distributions of the two enantiomers do not show appreciable differences. Theoretical and computational simulations provide us the basis to state that oriented enantiomers can be discriminated on-the-fly in photodissociation processes even initiated by non-circularly polarized light, provided that the three vectors encountered above have specific three-dimensional arrangements. The fact that Br fragment elimination involves a multi-potential dissociation carries uncertainties in theoretical estimates of the vector direction. Therefore, this work represents a preliminary but significant step on the road to chiral discrimination on-the-fly, which is shown to be best propitiated in molecules where vectors are far from having degenerate mutual angular directions.

A generalized unimolecular impulsive model for curved reaction path

This work aims to introduce a generalized impulsive model for unimolecular dissociation processes. This model allows us to take into account the curvature of the reaction path explicitly. It is a generalization of the previously developed multi-center impulsive model [P.-Y. Tsai and K.-C. Lin, J. Phys. Chem. A 119, 29 (2015)]. Several limitations of conventional impulsive models are eliminated by this study: (1) Unlike conventional impulsive models, in which a single molecular geometry is responsible for the impulse determination, the gradients on the whole dissociation path are taken into account. The model can treat dissociation pathways with large curvatures and loose saddle points. (2) The method can describe the vibrational excitation of polyatomic fragments due to the bond formation by multi-center impulse. (3) The available energy in conventional impulsive models is separated into uncoupled statistical and impulsive energy reservoirs, while the interplay between these reservoirs is allowed in the new model. (4) The quantum state correlation between fragments can be preserved in analysis. Dissociations of several molecular systems including the roaming pathways of formaldehyde, nitrate radical, acetaldehyde, and glyoxal are chosen as benchmarks. The predicted photofragment energy and vector distributions are consistent with the experimental results reported previously. In these examples, the capability of the new model to treat the curved dissociation path, loose saddle points, polyatomic fragments, and multiple-body dissociation is verified. As a cheaper computational tool with respect to ab initio on-the-fly direct dynamic simulations, this model can provide detailed information on the energy disposal, quantum state correlation, and stereodynamics in unimolecular dissociation processes.

Flexible or Robust Amorphous Photonic Crystals from Network-Forming Block Copolymers for Sensing Solvent Vapors

Large-area and flexible amorphous photonic crystals (APCs) featuring interconnected network microstructures are fabricated using high-molecular-weight polystyrene- block-poly(methyl methacrylate) (PS-PMMA) block copolymers. Kinetically controlled microphase separation combining with synergistic weak incompatibility gives rise to short-range-order network microstructures, exhibiting noniridescent optical properties. Solubility-dependent solvatochromism with distinct responses to various organic solvent vapors is observed in the network-forming APC film. By taking advantage of photodegradation of the PMMA block, nanoporous network-forming films were prepared for subsequent template synthesis of robust SiO₂- and TiO₂-based APC films through sol-gel reaction. Consequently, refractive index contrast of the APC film was able to be manipulated, resulting in intensely enhanced reflectivity and increased response rate for detecting solvent vapor. With the integration of self-assembly and photolithography approaches, flexible and robust network-forming APC films with well-defined photopatterned textures are carried out. This can provide a novel means for the design of photopatterned organic or inorganic APC films for sensing solvent vapors.

Photodissociation of CH3CHO at 248 nm: identification of the channels of roaming, triple fragmentation and the transition state

Quasi-classical trajectory (QCT) calculations are performed on the molecular products CO + CH₄via the tight transition state (TS) and global minimum configurations. With the aid of this theoretical evidence, we have re-examined the experimental results published previously to clarify the controversial issue of photodissociation dynamics of CH₃CHO at 248 nm. For the CO (v = 0 and 1) bimodal rotational distributions obtained previously [K.-C. Hung, P.-Y. Tsai, H.-K. Li, and K.-C. Lin, J. Chem. Phys., 2014, 140, 064313], the low-rotational (J) component is re-assigned to the contribution of triple fragmentation (H + CO + CH₃), whereas the high-J component is ascribed to the CH₃-roaming pathway. The H-roaming pathway is not found in the calculations. Further, the QCT results have confirmed that the CO vibrational population especially at higher states and the low-energy component of CH₄ vibrational bimodality obtained experimentally are mainly produced following the TS pathway, which has never been identified before. While taking into account both the theoretical and experimental results, the ratio of the molecular products (CO(v = 1) + CH₄) obtained by the triple fragmentation/roaming/TS processes is evaluated to be 0.23 : 1 : 0.29.

On the state selection of linear triatomic molecules by electrostatic hexapole fields

Electrostatic hexapole state-selector is a versatile tool in experimental stereodynamics. The requirement of appropriate models to correctly predict the behavior of molecules in the hexapole motivated us to realize a treatment that predicts the Stark effect of linear triatomic molecules with rotational doublet states. Various perturbative approximations are conventionally adopted to obtain analytic Stark energy derivatives of a truncated Hamiltonian matrix, without utilizing numerical diagonalization of the full Hamiltonian matrix. By including both the low and high field effects, which were alternatively ignored in the analytical formulae of such approximate approaches, herein we demonstrate that the performance of hexapole state selector to linear triatomic molecules can be appropriately predicted via Van Vleck transformation. This method can provide analytic Stark energy derivatives that are acceptably in consistent with the ones obtained via numerical diagonalization of the full Hamiltonian matrix. Particularly, this work is suitable for v2 = 1 level of linear triatomic molecules, due to the following reasons: (1) the Stark energy derivative and the molecular orientation as a function of the electric field are expressed in analytical formulae, hence it is suitable for implementation without involving numerical diagonalization of the full Hamiltonian matrix; (2) a better prediction of the focusing curves with respect to conventional analytical treatments is provided, allowing a reliable determination of the selected state compositions and molecular orientation.

Hexapole-Oriented Asymmetric-Top Molecules and Their Stereodirectional Photodissociation Dynamics

Molecular orientation is a fundamental requisite in the study of stereodirected dynamics of collisional and photoinitiated processes. In this past decade, variable hexapolar electric filters have been developed and employed for the rotational-state selection and the alignment of molecules of increasing complexity, for which the main difficulties are their mass, their low symmetry, and the very dense rotational manifold. In this work, for the first time, a complex molecule such as 2-bromobutane, an asymmetric top containing a heavy atom (the bromine), was successfully oriented by a weak homogeneous field placed downstream from the hexapolar filter. Efficiency of the orientation was characterized experimentally, by combining time-of-flight measurements and a slice-ion-imaging detection technique. The application is described to the photodissociation dynamics of the oriented 2-bromobutane, which was carried out at a laser wavelength of 234 nm, corresponding to the breaking of the C-Br bond. The Br photofragment is produced in both the ground Br ((2)P3/2) and the excited Br ((2)P1/2) electronic states, and both channels are studied by the slice imaging technique, revealing new features in the velocity and angular distributions with respect to previous investigations on nonoriented molecules.

Dynamical, spectroscopic and computational imaging of bond breaking in photodissociation: roaming and role of conical intersections

Recent experimental and theoretical advances in the study of the dissociation of excited molecules are revealing unexpected mechanisms, when their outcomes are tackled by combining (i) space-time ion imaging of translational features, with (ii) spectroscopic probing of rotational and vibrational distributions; crucial is the assistance of (iii) the quantum chemistry of structural investigations of rearrangements of chemical bonds, and of (iv) the simulations of molecular dynamics to follow the evolution of selective bond stretching and breaking. Here we present results of such an integrated approach to methyl formate, HCOOCH3, the simplest of esters; the main focus is on the rotovibrationally excited CO (v=1) product and in general on the energy distribution in the fragments. Previous laser studies of dissociation into CO and CH3OH at a sequence of various wavelengths discovered signatures of a roaming mechanism by the late arrival of CO (v=0) products in time-of-flight ion imaging. Subsequent detailed investigations as a function of excitation energy provided the assessment of the threshold, which opens for triple breakdown into CO and further fragments H and CH3O, as spectroscopically characterized by ion imaging and FTIR respectively. Accompanying quantum mechanical electronic structure calculations and classical molecular dynamics simulations clarify the origin of these fragments through "roaming" pathways involving incipient radical intermediates at energies below the triple fragmentation threshold: a specific role is played by nonadiabatic transitions at a conical intersection between ground and excited states; alternative pathways focalize our attention to regions of the potential energy surfaces other than those in the neighbourhoods of saddle points along minimum energy paths: eventually this leads us to look for avenues in reaction kinetics beyond those of venerable transition state theories.

Characterization of molecular channel in photodissociation of SOCl2 at 248 nm: Cl2 probing by cavity ring-down absorption spectroscopy

A primary elimination channel of the chlorine molecule in the one-photon dissociation of SOCl2 at 248 nm was investigated using cavity ring-down absorption spectroscopy (CRDS). By means of spectral simulation, the ratio of the vibrational population in the v = 0, 1, and 2 levels was evaluated to be 1 : (0.10 ± 0.02) : (0.009 ± 0.005), corresponding to a Boltzmann vibrational temperature of 340 ± 30 K. The Cl2 molecular channel was obtained with a quantum yield of 0.4 ± 0.2 from the X(1)A' ground state of SOCl2via internal conversion. The dissociation mechanism differs from a prior study where a smaller yield of <3% was obtained, initiated from the 2(1)A' excited state. Temperature-dependence measurements of the Cl2 fragment turn out to support our mechanism. With the aid of ab initio potential energy calculations, two dissociation routes to the molecular products were found, including one synchronous dissociation pathway via a three-center transition state (TS) and the other sequential dissociation pathway via a roaming-mediated isomerization TS. The latter mechanism with a lower energy barrier dominates the dissociation reaction.

Insight into photofragment vector correlation by a multi-center impulsive model

A multi-center impulsive model has been recently developed to characterize the dynamic feature of fragment vector correlation in photodissociation of formaldehyde, H₂CO → CO + H₂, via both transition state and roaming pathways.

Roaming as the dominant mechanism for molecular products in the photodissociation of large aliphatic aldehydes

Photodissociation of isobutyraldehyde (C₃H₇CHO) at 248 nm is investigated using time-resolved Fourier-transform infrared emission spectroscopy to demonstrate the growing importance of the roaming pathway with increasing molecular size of aliphatic aldehydes.

Molecular halogen elimination from halogen-containing compounds in the atmosphere

Atmospheric halogen chemistry has drawn much attention, because the halogen atom (X) playing a catalytic role may cause severe stratospheric ozone depletion. Atomic X elimination from X-containing hydrocarbons is recognized as the major primary dissociation process upon UV-light irradiation, whereas direct elimination of the X2 product has been seldom discussed or remained a controversial issue. This account is intended to review the detection of X2 primary products using cavity ring-down absorption spectroscopy in the photolysis at 248 nm of a variety of X-containing compounds, focusing on bromomethanes (CH2Br2, CF2Br2, CHBr2Cl, and CHBr3), dibromoethanes (1,1-C2H4Br2 and 1,2-C2H4Br2) and dibromoethylenes (1,1-C2H2Br2 and 1,2-C2H2Br2), diiodomethane (CH2I2), thionyl chloride (SOCl2), and sulfuryl chloride (SO2Cl2), along with a brief discussion on acyl bromides (BrCOCOBr and CH2BrCOBr). The optical spectra, quantum yields, and vibrational population distributions of the X2 fragments have been characterized, especially for Br2 and I2. With the aid of ab initio calculations of potential energies and rate constants, the detailed photodissociation mechanisms may be comprehended. Such studies are fundamentally important to gain insight into the dissociation dynamics and may also practically help to assess the halogen-related environmental variation.

Photodissociation of Propionaldehyde at 248 nm: Roaming Pathway as an Increasingly Important Role in Large Aliphatic Aldehydes

Time-resolved Fourier transform infrared emission spectroscopy is employed in the photolysis of propionaldehyde (CH3CH2CHO) at 248 nm to characterize the role of the roaming pathway. High-resolution spectra of CO are analyzed to yield a single Boltzmann rotational distribution for each vibrational level (ν = 1-4) with small rotational and large vibrational energy disposals. A roaming saddle point is found containing two far separated moieties of HCO and CH3CH2 with a weak interaction between them. Quasiclassical trajectory calculations on this configuration yield the CO energy flow behavior, consistent with the findings. The rate constant along the roaming pathway is evaluated to be larger by >1-2 orders of magnitude than those along tight transition state or three-body dissociation pathways. This work implies that the roaming mechanism plays an increasingly important role in aliphatic aldehydes as the molecular size becomes larger.

Alignment selection of the metastable CO(a 3Π1) molecule and the steric effect in the aligned CO(a 3Π1) + NO collision

The aligned metastable CO(a (3)Π1) molecular beam was generated by an electronic excitation through the Cameron band (CO a (3)Π1 ← X (1)Σ(+)) transition. Beam characterization of the aligned molecular beam of CO(a (3)Π1) was carried out by (1 + 1) REMPI detection via the b (3)Σ(+) state. The REMPI signals showed the clear dependence on the polarization of the pump laser, and the experimental result was well reproduced by the theoretical simulation. This agreement confirms that aligned metastable CO(a (3)Π1) can be generated and controlled by rotating polarization of the pump laser. By using this technique, a single quantum state of CO(a (3)Π1) can be selected as a metastable molecular beam. The steric effect in the energy-transfer collision of CO(a (3)Π1) with NO forming the excited NO was carried out with this aligned CO(a (3)Π1) molecular beam. We find that the sideways orientation of CO(a (3)Π1) is more favorable in the formation of the excited NO(A (2)Σ(+), B (2)Π) than that for the axial collisions. The obtained steric effect was discussed with the aid of the spatial distribution of CO(a (3)Π1) molecular orbitals, and we find that specific rotational motion of CO(a (3)Π1) in each state may not be a dominant factor in this energy-transfer collision.

Note: Photodissociation of CH3COCN at 308 nm by time-resolved Fourier-transform infrared emission spectroscopy: is CO a primary or secondary product?

This Note aims to clarify the source of CO in photodissociation of acetyl cyanide (CH3COCN) at 308 nm. From the theoretical aspects, a new pathway via isomerization transition state (TS) at 391 ± 8 kJ∕mol is found leading to the CO + CH3NC products. An amount of 60% reactant molecules at 300 K is estimated to successfully surpass the average TS barrier lying above the excitation energy by 3.5 kJ∕mol. Further, a prior distribution method is conducted to characterize the vibrational energy distribution of CO on a statistical basis. The pathway to CH3NC + CO yields a vibrational branching ratio (v = 0:v = 1:v = 2:v = 3∼0.63:0.25:0.093:0.032) in excellent agreement with the observation (0.62:0.25:0.09:0.05).

Competitive bond rupture in the photodissociation of bromoacetyl chloride and 2- and 3-bromopropionyl chloride: adiabatic versus diabatic dissociation

Competitive bond dissociation mechanisms for bromoacetyl chloride and 2- and 3-bromopropionyl chloride following the (1) [n(O)→π*(C=O)] transition at 234-235 nm are investigated. Branching ratios for C−Br/C−Cl bond fission are found by using the (2+1) resonance-enhanced multiphoton ionization (REMPI) technique coupled with velocity ion imaging. The fragment branching ratios depend mainly on the dissociation pathways and the distances between the orbitals of Br and the C=O chromophore. C−Cl bond fission is anticipated to follow an adiabatic potential surface for a strong diabatic coupling between the n(O)π*(C=O) and np (Cl)σ*(C−Cl) bands. In contrast, C−Br bond fission is subject to much weaker coupling between n(O)π*(C=O) and np (Br)σ*(C−Br). Thus, a diabatic pathway is preferred for bromoacetyl chloride and 2-bromopropionyl chloride, which leads to excited-state products. For 3-bromopropionyl chloride, the available energy is not high enough to reach the excited-state products such that C−Br bond fission must proceed through an adiabatic pathway with severe suppression by nonadiabatic coupling. The fragment translational energies and anisotropy parameters for the three molecules are also analyzed and appropriately interpreted.