Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa.

Improving our understanding of host­microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the three-dimensional (3D) spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 d after recovery when overall bacterial loads returned to preantibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern is resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that Lactobacilli were found closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, regardless of antibiotic exposure. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.

Spatial Genomic Analysis: A Multiplexed Transcriptional Profiling Method that Reveals Subpopulations of Cells Within Intact Tissues.

Here, we present Spatial Genomic Analysis (SGA), a quantitative single-cell transcriptional profiling method that takes advantage of single-molecule imaging of individual transcripts for up to a hundred genes. SGA relies on a machine learning-based image analysis pipeline that performs cell segmentation and transcript counting in a robust way. SGA is suitable for various in situ applications and was originally developed to address heterogeneity in the neural crest, which is a transient embryonic stem cell population important for formation of various vertebrate body structures. After being specified as multipotent neural crest stem cells in the dorsal neural tube, they go through an epithelial to mesenchymal transition in order to migrate to different destinations around the body, and gradually turn from stem cells to progenitors prior to final commitment. The molecular details of this process remain largely unknown, and upon their emergence, the neural crest cells have been considered as a single homogeneous population. Technical limitations have restricted the possibility to parse the neural crest cell pool into subgroups according to multiplex gene expression properties. By using SGA, we were able to identify subgroups inside the neural crest niche in the dorsal neural tube. The high sensitivity of the method allows detection of low expression levels and we were able to determine factors not previously shown to be present in neural crest stem cells, such as pluripotency or lineage markers. Finally, SGA analysis also provides prediction of gene relationships within individual cells, and thus has broad utility for powerful transcriptome analyses in original biological contexts.

Identification of a neural crest stem cell niche by Spatial Genomic Analysis.

The neural crest is an embryonic population of multipotent stem cells that form numerous defining features of vertebrates. Due to lack of reliable techniques to perform transcriptional profiling in intact tissues, it remains controversial whether the neural crest is a heterogeneous or homogeneous population. By coupling multiplex single molecule fluorescence in situ hybridization with machine learning algorithm based cell segmentation, we examine expression of 35 genes at single cell  resolution in vivo. Unbiased hierarchical clustering reveals five spatially distinct subpopulations within the chick dorsal neural tube. Here we identify a neural crest stem cell niche that centers around the dorsal midline with high expression of neural crest genes, pluripotency factors, and lineage markers. Interestingly, neural and neural crest stem cells express distinct pluripotency signatures. This Spatial Genomic Analysis toolkit provides a straightforward approach to study quantitative multiplex gene expression in numerous biological systems, while offering insights into gene regulatory networks via synexpression analysis.

Directed Evolution of a Bright Near-Infrared Fluorescent Rhodopsin Using a Synthetic Chromophore.

By engineering a microbial rhodopsin, Archaerhodopsin-3 (Arch), to bind a synthetic chromophore, merocyanine retinal, in place of the natural chromophore all-trans-retinal (ATR), we generated a protein with exceptionally bright and unprecedentedly red-shifted near-infrared (NIR) fluorescence. We show that chromophore substitution generates a fluorescent Arch complex with a 200-nm bathochromic excitation shift relative to ATR-bound wild-type Arch and an emission maximum at 772 nm. Directed evolution of this complex produced variants with pH-sensitive NIR fluorescence and molecular brightness 8.5-fold greater than the brightest ATR-bound Arch variant. The resulting proteins are well suited to bacterial imaging; expression and stability have not been optimized for mammalian cell imaging. By targeting both the protein and its chromophore, we overcome inherent challenges associated with engineering bright NIR fluorescence into Archaerhodopsin. This work demonstrates an efficient strategy for engineering non-natural, tailored properties into microbial opsins, properties relevant for imaging and interrogating biological systems.

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.

Accurate and robust detection of mRNA molecules in thick tissue samples can reveal gene expression patterns in single cells within their native environment. Preserving spatial relationships while accessing the transcriptome of selected cells is a crucial feature for advancing many biological areas - from developmental biology to neuroscience. However, because of the high autofluorescence background of many tissue samples, it is difficult to detect single-molecule fluorescence in situ hybridization (smFISH) signals robustly in opaque thick samples. Here, we draw on principles from the emerging discipline of dynamic nucleic acid nanotechnology to develop a robust method for multi-color, multi-RNA imaging in deep tissues using single-molecule hybridization chain reaction (smHCR). Using this approach, single transcripts can be imaged using epifluorescence, confocal or selective plane illumination microscopy (SPIM) depending on the imaging depth required. We show that smHCR has high sensitivity in detecting mRNAs in cell culture and whole-mount zebrafish embryos, and that combined with SPIM and PACT (passive CLARITY technique) tissue hydrogel embedding and clearing, smHCR can detect single mRNAs deep within thick (0.5 mm) brain slices. By simultaneously achieving ∼20-fold signal amplification and diffraction-limited spatial resolution, smHCR offers a robust and versatile approach for detecting single mRNAs in situ, including in thick tissues where high background undermines the performance of unamplified smFISH.

Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

To facilitate fine-scale phenotyping of whole specimens, we describe here a set of tissue fixation-embedding, detergent-clearing and staining protocols that can be used to transform excised organs and whole organisms into optically transparent samples within 1-2 weeks without compromising their cellular architecture or endogenous fluorescence. PACT (passive CLARITY technique) and PARS (perfusion-assisted agent release in situ) use tissue-hydrogel hybrids to stabilize tissue biomolecules during selective lipid extraction, resulting in enhanced clearing efficiency and sample integrity. Furthermore, the macromolecule permeability of PACT- and PARS-processed tissue hybrids supports the diffusion of immunolabels throughout intact tissue, whereas RIMS (refractive index matching solution) grants high-resolution imaging at depth by further reducing light scattering in cleared and uncleared samples alike. These methods are adaptable to difficult-to-image tissues, such as bone (PACT-deCAL), and to magnified single-cell visualization (ePACT). Together, these protocols and solutions enable phenotyping of subcellular components and tracing cellular connectivity in intact biological networks.

Mixing of the immiscible: hydrocarbons in water-ice near the ice crystallization temperature.

Structural changes in hydrocarbon-doped water-ice during amorphous to crystalline phase conversion are investigated using polycyclic aromatic hydrocarbons (PAHs) as probes. We show that aggregation of impurity molecules occurs due to the amorphous-crystalline transition in ice, especially when they are hydrophobic molecules such as PAHs. Using ultraviolet-visible (UV-vis), Fourier-transform Infrared (FTIR), and laser-induced-fluorescence (LIF) spectroscopic techniques, we show that, although ice infrared absorption features change from a broad structureless band corresponding to amorphous ice to a sharp structured crystalline ice bands, simultaneously, sharper isolated PAH UV absorption features measured in the amorphous ice host turn broad upon ice crystallization. A simultaneous decrease in the monomer fluorescence and increase in the excimer emission band is observed, a clear indication for the formation of PAH molecular aggregates when amorphous ice is converted to crystalline ice at higher temperatures. Similar to the irreversible amorphous-crystalline phase transitions, the UV, fluorescence, and excimer emissions indicate that PAHs undergo irreversible aggregation. Our studies suggest that organic impurities exist as aggregates rather than monomers trapped in crystalline water-ice when cycled through temperatures that convert amorphous ice to crystalline ice, rendering a better insight into phenomena such as the formation of cometary crust. This aggregate formation also may significantly change the secondary reaction pathways and rates in impurity-doped ices in the lab, on Earth, in the solar system, and in the interstellar medium.

Matrix effect on vibrational frequencies: experiments and simulations for HCl and HNgCl (Ng = Kr and Xe).

We study the environmental effect on molecules embedded in noble-gas (Ng) matrices. The experimental data on HXeCl and HKrCl in Ng matrices is enriched. As a result, the H-Xe stretching bands of HXeCl are now known in four Ng matrices (Ne, Ar, Kr, and Xe), and HKrCl is now known in Ar and Kr matrices. The order of the H-Xe stretching frequencies of HXeCl in different matrices is ν(Ne) < ν(Xe) < ν(Kr) < ν(Ar), which is a non-monotonous function of the dielectric constant, in contrast to the "classical" order observed for HCl: ν(Xe) < ν(Kr) < ν(Ar) < ν(Ne). The order of the H-Kr stretching frequencies of HKrCl is consistently ν(Kr) < ν(Ar). These matrix effects are analyzed theoretically by using a number of quantum chemical methods. The calculations on these molecules (HCl, HXeCl, and HKrCl) embedded in single Ng(') layer cages lead to very satisfactory results with respect to the relative matrix shifts in the case of the MP4(SDQ) method whereas the B3LYP-D and MP2 methods fail to fully reproduce these experimental results. The obtained order of frequencies is discussed in terms of the size available for the Ng hydrides in the cages, probably leading to different stresses on the embedded molecule. Taking into account vibrational anharmonicity produces a good agreement of the MP4(SDQ) frequencies of HCl and HXeCl with the experimental values in different matrices. This work also highlights a number of open questions in the field.

Environmental effects on noble-gas hydrides: HXeBr, HXeCCH, and HXeH in noble-gas and molecular matrices.

Noble-gas hydrides HNgY (Ng is a noble-gas atom and Y is an electronegative group) are sensitive probes of local environment due to their relatively weak bonding and large dipole moments. We experimentally studied HXeBr in Ar, Kr, and N2 matrices, HXeCCH in Ne and N2 matrices, and HXeH in an N2 matrix. These are the first observations of noble-gas hydrides in an N2 matrix. An N2 matrix strongly increases the H-Xe stretching frequency of HXeBr and HXeCCH with respect to a Ne matrix, which is presumably due to a strong interaction between the HNgY dipole moment and quadrupole moments of the surrounding lattice N2 molecules. The spectral shift of HXeBr in an N2 matrix is similar to that in a CO2 matrix, which is a rather unexpected result because the quadrupole moment of CO2 is about three times as large as that of N2. The H-Xe stretching frequencies of HXeBr and HXeCCH in noble-gas matrices show a trend of ν(Ne) < ν(Xe) < ν(Kr) < ν(Ar), which is a non-monotonous function of the dielectric constants of the noble-gas solids. The MP2(full) calculations of HXeBr and HXeCCH with the polarizable continuum model as well as the CCSD(T) calculations of the HXeBr···Ng and HXeCCH···Ng (Ng = Ne, Ar, Kr, and Xe) complexes cannot fully explain the experimental observations. It is concluded that more sophisticated computational models should be used to describe these experimental findings.

Photochemical activity of Titan's low-altitude condensed haze.

Titan, the largest moon of Saturn and similar to Earth in many aspects, has unique orange-yellow colour that comes from its atmospheric haze, whose formation and dynamics are far from well understood. Present models assume that Titan's tholin-like haze formation occurs high in atmosphere through gas-phase chemical reactions initiated by high-energy solar radiation. Here we address an important question: Is the lower atmosphere of Titan photochemically active or inert? We demonstrate that indeed tholin-like haze formation could occur on condensed aerosols throughout the atmospheric column of Titan. Detected in Titan's atmosphere, dicyanoacetylene (C4N2) is used in our laboratory simulations as a model system for other larger unsaturated condensing compounds. We show that C4N2 ices undergo condensed-phase photopolymerization (tholin formation) at wavelengths as long as 355 nm pertinent to solar radiation reaching a large portion of Titan's atmosphere, almost close to the surface.

Halogenated xenon cyanides ClXeCN, ClXeNC, and BrXeCN.

We report on the preparation and characterization of three new noble-gas molecules ClXeCN, ClXeNC, and BrXeCN. These molecules are synthesized by 193 nm photolysis and thermal annealing of ClCN and BrCN in a xenon matrix. The absorption spectra are measured in the mid- and far-infrared regions, and the assignment is supported by isotope substitution and quantum chemical calculations at the B3LYP and MP2 levels of theory. The present results demonstrate a way to prepare other noble-gas molecules of this type.

HY...N2 and HXeY...N2 complexes in solid xenon (Y=Cl and Br): unexpected suppression of the complex formation for deposition at higher temperature.

The 1:1 complexes of HY and HXeY (Y=Cl and Br) with nitrogen are characterized by FTIR spectroscopy in a Xe matrix. These complexes show small blue shifts of the HY and H-Xe stretching frequencies with respect to the monomers (ca. +10 cm(-1)). In the HXeY...N(2) synthesis procedure, a HY/N(2)/Xe matrix with HY...N(2) complexes is first photolyzed at 193 nm to yield isolated H and Y...N(2) fragments. At the second step, annealing at ca. 40 K activates mobility of H atoms and promotes the H+Xe+Y...N(2) reaction. It is quite remarkable that the HY...N(2) and consequently HXeY...N(2) complexes are observed in Xe matrices deposited at relatively low temperature (below ca. 35 K). For Xe matrices deposited above ca. 40 K, HY molecules do not form a complex with nitrogen and the HXeY...N(2) complex does not appear after photolysis and annealing; however, this observation is not explained in this article.

Matrix-isolation and Ab initio study of the HKrCl...HCl complex.

The HKrCl complex with HCl is characterized by IR spectroscopy in a Kr matrix and by ab initio calculations. The HKrCl...HCl complex exhibits a strong blue shift of the H-Kr stretching mode in comparison with the HKrCl monomer, which indicates stabilization of the H-Kr bond upon complexation. The obtained maximal shift of ca. +300 cm(-1) is probably the largest blue shift experimentally observed for 1:1 molecular complexes. The HCl absorptions are found to be strongly red-shifted upon complexation with HKrCl (up to ca. -500 cm(-1)). In the HKrCl synthesis procedure, an HCl/Kr matrix was first photolyzed at 193 nm to yield H and Cl atoms in a Kr matrix and then annealed at about 30 K to activate mobility of H atoms and to promote the H + Kr + Cl reaction. The HKrCl...HCl complex is mainly formed from the Cl...HCl intermediate complex that is produced by photolysis of HCl dimers. Bands of the HKrCl...(HCl)(2) complex are tentatively identified with a very large shift of ca. +700 cm(-1) for the H-Kr stretching mode. These experimental observations are supported and explained by ab initio calculations.

Experimental and computational study of HXeY...HX complexes (X, Y = Cl and Br): an example of exceptionally large complexation effect.

The complexes of xenon hydrides HXeY (Y = Cl and Br) with hydrogen halides HX (X = Cl and Br) have been studied both computationally and experimentally in a xenon matrix. The experiments revealed three new complexes: HXeBr...HBr, HXeBr...HCl, and HXeCl...HCl. The experimental assignments were done on the basis of the strong H-Xe stretching absorption of HXeY (Y = Cl and Br) molecules and supported by theoretical results. We experimentally obtained monomer-to-complex blue-shifts of this vibrational mode for all the studied systems (up to approximately 150 cm (-1)). The electronic structure calculations revealed three local structures for each HNgY...HX complexes and their computed interaction energies varied between -460 and -2800 cm (-1). The computational estimates of the vibrational shifts were in agreement with the experimental values. We also found possible experimental absorption belonging to HXeBr...(HBr) 2 trimer and its vibrational shift (+245 cm (-1)) is similar to the computational estimate of a cyclic ternary complex (+252 cm (-1)).

Formation of noble-gas hydrides and decay of solvated protons revisited: diffusion-controlled reactions and hydrogen atom losses in solid noble gases.

UV photolysis and annealing of C2H2/Xe, C2H2/Xe/Kr, and HBr/Xe matrices lead to complicated photochemical processes and reactions. The dominating products in these experiments are noble-gas hydrides with general formula HNgY (Ng = noble-gas atom, Y = electronegative fragment). We concentrate on distinguishing the local and global mobility and losses of H atoms, barriers of the reactions, and the decay of solvated protons. Different deposition temperatures change the amount of lattice imperfections and thus the amount of traps for H atoms. The averaged distance between reacting species influencing the reaction kinetics is controlled by varying the precursor concentration. A number of solid-state processes connected to the formation of noble-gas hydrides and decay of solvated protons are discussed using a simple kinetic model. The most efficient formation of noble-gas hydrides is connected with global (long-range) mobility of H atoms leading to the H + Xe + Y reaction. The highest concentration of noble-gas hydrides was obtained in matrices of highest optical quality, which probably have the lowest concentration of defects and H-atom losses. In matrices with high amount of geometrical imperfections, the product formation is inefficient and dominated by a local (short-range) process. The decay of solvated protons is rather local than a global process, which is different from the formation of noble-gas molecules. However, the present data do not allow distinguishing local proton and electron mobilities. Our previous results indicate that these are electrons which move to positively-charged centers and neutralize them. It is believed that the image obtained here for solid xenon is applicable to solid krypton whereas the case of argon deserves special attention.

Matrix isolation and ab initio study of the HXeCCH...CO2 complex.

The HXeCCH...CO2 complex is studied experimentally and computationally. The complex is prepared in a low-temperature xenon matrix using UV photolysis of propiolic acid (HCCCOOH) and thermal mobilization of H atoms at 45 K. Photolysis of propiolic acid leads to the HCCH...CO2 complex as one of the photolysis products. The HCCH...CO2 complex is further photolyzed to the HCC...CO2 complex. Thermal annealing leads to the formation of HXeCCH complexed with CO2. The H-Xe stretching absorption of the HXeCCH...CO2 complex is blueshifted (+31.9 and +5.8 cm(-1)) from the value of the HXeCCH monomer in a xenon matrix. In the calculations, three HXeCCH...CO2 structures were found (one parallel and two linear structures) corresponding to the true energy minima on the potential energy surface. For the H-Xe stretching mode, the calculations give blueshifted values of +19.2 or +19.5 cm(-1) depending on the computational level [MP2/6-311++G(2d,2p) and MP2/aug-cc-pVDZ] for the parallel structure and +19.4 or +27.9 cm(-1) for one linear structure. For the second linear structure, the H-Xe stretching frequency is redshifted by -8.6 or -9.4 cm(-1) at these levels of theory. Based on the calculations, the experimental band shifted by +5.8 cm(-1) (1492.2 cm(-1)) most likely corresponds to the HXeCCH...CO2 parallel structure. The band with larger blueshift of +31.9 cm(-1) (1518.3 cm(-1)) can be due to another matrix site of the same structure or to the blueshifting linear structure.

On theoretical predictions of noble-gas hydrides.

We discuss the present status and reliability of theoretical predictions of noble-gas hydride molecules. It is shown that the single-reference MP2 calculations can produce a rather inaccurate energy diagram for the formation of noble-gas hydrides, and this may mislead the theoretical predictions. We suggest that the computational dissociation energy of the HY precursors should always be compared with the experimental values as a checkpoint for the computational accuracy. The computational inaccuracy probably explains why some compounds that are stable with the single-reference MP2 method (HArC(4)H, HArC(3)N, and HArCN) did not appear in matrix-isolation experiments, whereas the corresponding compounds with Kr and Xe are known.

Insertion of noble gas atoms into cyanoacetylene: an ab initio and matrix isolation study.

A computational and experimental matrix isolation study of insertion of noble gas atoms into cyanoacetylene (HCCCN) is presented. Twelve novel noble gas insertion compounds are found to be kinetically stable at the MP2 level of theory, including four molecules with argon. The first group of the computationally studied molecules belongs to noble gas hydrides (HNgCCCN and HNgCCNC), and we found their stability for Ng = Ar, Kr, and Xe. The HNgCCCN compounds with Kr and Xe have similar stability to that of previously reported HKrCN and HXeCN. The HArCCCN molecule seems to have a weaker H-Ar bond than in the previously identified HArF molecule. The HNgCCNC molecules are less stable than the HNgCCCN isomers for all noble gas atoms. The second group of the computational insertion compounds, HCCNgCN and HCCNgNC, are of a different type, and they also are kinetically stable for Ng = Ar, Kr, and Xe. Our photolysis and annealing experiments with low-temperature cyanoacetylene/Ng (Ng = Ar, Kr, and Xe) matrixes evidence the formation of two noble gas hydrides for Ng = Kr and Xe, with the strongest IR absorption bands at 1492.1 and 1624.5 cm(-1), and two additional absorption modes for each species are found. The computational spectra of HKrCCCN and HXeCCCN fit most closely the experimental data, which is the basis for our assignment. The obtained species absorb at quite similar frequencies as the known HKrCN and HXeCN molecules, which is in agreement with the theoretical predictions. No strong candidates for an Ar compound are observed in the IR absorption spectra. As an important side product of this work, the data obtained in long-term decay of KrHKr+ cations suggest a tentative assignment for the CCCN radical.

Protons solvated in noble-gas matrices: interaction with nitrogen.

The interaction of a (NgHNg)(+) cation (Ng = Ar and Kr) with a nitrogen molecule is studied. The structure, energetics, and vibrational properties of these complexed systems are computationally studied at the MP2/6-311++G(2d,2p) level of theory. The computations reveal two stable structures, linear and T-shaped configurations, with BSSE corrected interaction energies of the order of -1000 cm(-1). The (NgHNg)(+)[dot dot dot]N(2) complexes are characterized experimentally by IR absorption spectroscopy in solid Ar and Kr matrices. The spectra show that only one complex structure is present, as evidenced by the single nitrogen-induced nu(3) band. According to the computational results, the linear structure is more probable in the experiments. However, our results show that the one-to-one complex at the present computational level does not accurately agree with the matrix-isolation experiments, the differences originating possibly from the influence of the surrounding matrix. Based on the current data, the mechanism of cation decay in noble-gas matrices is discussed. The observed similar decay of (NgHNg)(+) and its N(2) complex indicates that the solvated proton is unable to tunnel and is therefore immobile in noble-gas matrices. The observations for the cation decay are consistent with the electron neutralization mechanism.

Neutralization of solvated protons and formation of noble-gas hydride molecules: matrix-isolation indications of tunneling mechanisms?

The (NgHNg)+ cations (Ng = Ar and Kr) produced via the photolysis of HFAr, HFKr, and HBrKr solid mixtures are studied, with emphasis on their decay mechanisms. The present experiments provide a large variety of parameters connected to this decay phenomenon, which allows us to reconsider various models for the decay of the (NgHNg)+ cations in noble-gas matrices. As a result, we propose that this phenomenon could be explained by the neutralization of the solvated protons by electrons. The mechanism of this neutralization reaction probably involves tunneling of an electron from an electronegative fragment or another trap to the (NgHNg)+ cation. The proposed electron-tunneling mechanism should be considered as a possible alternative to the literature models based on tunneling-assisted or radiation-induced diffusion of protons in noble-gas solids. As a novel experimental observation of this work, the efficient formation of HArF molecules occurs at 8 K in a photolyzed HFAr matrix. It is probable that the low-temperature formation of HArF involves local tunneling of the H atom to the Ar-F center, which in turn supports the locality of HF photolysis in solid Ar. In this model, the decay of (ArHAr)+ ions and the formation of HArF molecules observed at low temperatures are generally unconnected processes; however, the decaying (ArHAr)+ ions may contribute to some extent to the formation of HArF molecules.