Transcriptome dynamics of developing maize leaves and genomewide prediction of cis elements and their cognate transcription factors.

Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize leaves from dry seeds to 192 h post imbibition, we studied gene up- and down-regulation and functional transition during leaf development and inferred sets of strongly coexpressed genes. More significantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cognate transcription factors (TFs) using genomic sequence and transcriptomic data. The method requires not only evolutionary conservation of candidate TFBSs and sets of strongly coexpressed genes but also that the genes in a gene set share the same Gene Ontology term so that they are involved in the same biological function. In addition, we developed another method to predict maize TF-TFBS pairs using known TF-TFBS pairs in Arabidopsis or rice. From these efforts, we predicted 1,340 novel TFBSs and 253 new TF-TFBS pairs in the maize genome, far exceeding the 30 TF-TFBS pairs currently known in maize. In most cases studied by both methods, the two methods gave similar predictions. In vitro tests of 12 predicted TF-TFBS interactions showed that our methods perform well. Our study has significantly expanded our knowledge on the regulatory network involved in maize leaf development.

Photoelectron Spectroscopy of the Methide Anion: Electron Affinities of (•)CH3 and (•)CD3 and Inversion Splittings of CH3(-) and CD3(-).

We report high-resolution photoelectron spectra of the simplest carbanions, CH3⁻ and CD3⁻. The vibrationally resolved spectra are dominated by a long progression in the umbrella mode (ν2) of ˙CH3 and ˙CD3, indicating a transition from a pyramidal C(3v) anion to the planar D(3h) methyl radical. Analysis of the spectra provides electron affinities of ˙CH3 (0.093(3) eV) and ˙CD3 (0.082(4) eV). These results enable improved determination of the corresponding gas-phase acidities: Δ(acid)H(0K)°(CH4) = 414.79(6) kcal/mol and Δ(acid)H(0K)°(CD4) = 417.58(8) kcal/mol. On the basis of the photoelectron anisotropy distribution, the electron is photodetached from an orbital with predominant p-character, consistent with the sp³-hybridized orbital picture of the pyramidal anion. The double-well potential energy surface along the umbrella inversion coordinate leads to a splitting of the vibrational energy levels of the umbrella mode. The inversion splittings of CH3⁻ and CD3⁻ are 21(5) and 6(4) cm⁻¹, respectively, and the corresponding anion umbrella vibrational frequencies are 444(13) and 373(12) cm⁻¹, respectively. Quantum mechanical calculations reported herein show good agreement with the experimental data and provide insight regarding the electronic potential energy surface of CH3⁻.

A versatile, pulsed anion source utilizing plasma-entrainment: characterization and applications.

A novel pulsed anion source has been developed, using plasma entrainment into a supersonic expansion. A pulsed discharge source perpendicular to the main gas expansion greatly reduces unwanted "heating" of the main expansion, a major setback in many pulsed anion sources in use today. The design principles and construction information are described and several examples demonstrate the range of applicability of this anion source. Large OH(-)(Ar)n clusters can be generated, with over 40 Ar solvating OH(-). The solvation energy of OH(-)(Ar)n, where n = 1-3, 7, 12, and 18, is derived from photoelectron spectroscopy and shows that by n = 12-18, each Ar is bound by about 10 meV. In addition, cis- and trans- HOCO(-) are generated through rational anion synthesis (OH(-) + CO + M → HOCO(-) + M) and the photoelectron spectra compared with previous results. These results, along with several further proof-of-principle experiments on solvation and transient anion synthesis, demonstrate the ability of this source to efficiently produce cold anions. With modifications to two standard General Valve assemblies and very little maintenance, this anion source provides a versatile and straightforward addition to a wide array of experiments.

Electronic states of the quasilinear molecule propargylene (HCCCH) from negative ion photoelectron spectroscopy.

We use gas-phase negative ion photoelectron spectroscopy to study the quasilinear carbene propargylene, HCCCH, and its isotopologue DCCCD. Photodetachment from HCCCH­ affords the X̃(3B) ground state of HCCCH and its ã(1A), b̃ (1B), d̃(1A2), and B̃(3A2) excited states. Extended, negatively anharmonic vibrational progressions in the X̃(3B) ground state and the open-shell singlet b̃ (1B) state arise from the change in geometry between the anion and the neutral states and complicate the assignment of the origin peak. The geometry change arising from electron photodetachment results in excitation of the ν4 symmetric CCH bending mode, with a measured fundamental frequency of 363 ± 57 cm(­1) in the X̃(3B) state. Our calculated harmonic frequency for this mode is 359 cm(­1). The Franck­Condon envelope of this progression cannot be reproduced within the harmonic approximation. The spectra of the ã(1A), d̃(1A2), and B̃(3A2) states are each characterized by a short vibrational progression and a prominent origin peak, establishing that the geometries of the anion and these neutral states are similar. Through comparison of the HCCCH­ and DCCCD­ photoelectron spectra, we measure the electron affinity of HCCCH to be 1.156 ± (0.095)(0.010) eV, with a singlet­triplet splitting between the X̃(3B) and the ã(1A) states of ΔEST = 0.500 ± (0.01)(0.10) eV (11.5 ± (0.2)(2.3) kcal/mol). Experimental term energies of the higher excited states are T0 [b̃(1B)] = 0.94 ± (0.20)(0.22) eV, T0 [d̃(1A2)] = 3.30 ± (0.02)(0.10) eV, T0 [B̃(3A2)] = 3.58 ± (0.02)(0.10) eV. The photoelectron angular distributions show significant π character in all the frontier molecular orbitals, with additional σ character in orbitals that create the X̃(3B) and b̃(1B) states upon electron detachment. These results are consistent with a quasilinear, nonplanar, doubly allylic structure of X̃(3B) HCCCH with both diradical and carbene character.

PTEN interacts with metal-responsive transcription factor 1 and stimulates its transcriptional activity.

MTF-1 (metal-responsive transcription factor 1) is an essential mammalian protein for embryonic development and modulates the expression of genes involving in zinc homoeostasis and responding to oxidative stress. We report in the present paper that PTEN (phosphatase and tensin homologue deleted on chromosome 10) associates with MTF-1 in the cells. These two proteins interact via the acidic domain of MTF-1 and the phosphatase/C2 domain of PTEN. Depletion of PTEN reduced MT (metallothionein) gene expression and increased cellular sensitivity to cadmium toxicity. PTEN did not alter the nuclear translocation, protein stability or DNA-binding activity of MTF-1. Zinc increased MTF-1-PTEN interaction in a dose-dependent manner. The interaction elevated within 2 h of zinc addition and declined afterwards in the cells. The enhanced binding activity occurred mainly in the cytoplasm and reduced after translocating the MTF-1 into the nucleus. Blocking signalling through the PI3K (phosphoinositide 3-kinase) pathway did not alter the zinc-induced MT expression. Analysis of enzymatically inactive PTEN mutants demonstrated that protein but not lipid phosphatase activity of PTEN was involved in the regulation of MTF-1 activity. The same regulatory role of PTEN was also noted in the regulation of ZnT1 (zinc transporter 1), another target gene of MTF-1.

New view of the ICN A continuum using photoelectron spectroscopy of ICN-.

Negative-ion photoelectron spectroscopy of ICN(-) (X̃ (2)Σ(+)) reveals transitions to the ground electronic state (X̃ (1)Σ(+)) of ICN as well as the first five excited states ((3)Π(2), (3)Π(1), Π(0(-) ) (3), Π(0(+) ) (3), and (1)Π(1)) that make up the ICN A continuum. By starting from the equilibrium geometry of the anion, photoelectron spectroscopy characterizes the electronic structure of ICN at an elongated I-C bond length of 2.65 Å. Because of this bond elongation, the lowest three excited states of ICN ((3)Π(2), (3)Π(1), and Π(0(-) ) (3)) are resolved for the first time in the photoelectron spectrum. In addition, the spectrum has a structured peak that arises from the frequently studied conical intersection between the Π(0(+) ) (3) and (1)Π(1) states. The assignment of the spectrum is aided by MR-SO-CISD calculations of the potential energy surfaces for the anion and neutral ICN electronic states, along with calculations of the vibrational levels supported by these states. Through thermochemical cycles involving spectrally narrow transitions to the excited states of ICN, we determine the electron affinity, EA(ICN), to be 1.34(5) (+0.04∕-0.02) eV and the anion dissociation energy, D(0)(X̃ (2)Σ(+) I-CN(-)), to be 0.83 (+0.04/-0.02) eV.

Ground and low-lying excited states of propadienylidene (H2C=C=C:) obtained by negative ion photoelectron spectroscopy.

A joint experimental-theoretical study has been carried out on electronic states of propadienylidene (H(2)CCC), using results from negative-ion photoelectron spectroscopy. In addition to the previously characterized X(1)A(1) electronic state, spectroscopic features are observed that belong to five additional states: the low-lying ã(3)B(1) and b(3)A(2) states, as well as two excited singlets, Ã(1)A(2) and B(1)B(1), and a higher-lying triplet, c(3)A(1). Term energies (T(0), in cm(-1)) for the excited states obtained from the data are: 10,354±11 (ã(3)B(1)); 11,950±30 (b(3)A(2)); 20,943±11 (c(3)A(1)); and 13,677±11 (Ã(1)A(2)). Strong vibronic coupling affects the Ã(1)A(2) and B(1)B(1) states as well as ã(3)B(1) and b(3)A(2) and has profound effects on the spectrum. As a result, only a weak, broadened band is observed in the energy region where the origin of the B(1)B(1) state is expected. The assignments here are supported by high-level coupled-cluster calculations and spectral simulations based on a vibronic coupling Hamiltonian. A result of astrophysical interest is that the present study supports the idea that a broad absorption band found at 5450 Å by cavity ringdown spectroscopy (and coincident with a diffuse interstellar band) is carried by the B(1)B(1) state of H(2)CCC.

Dynamic mapping of CN rotation following photoexcitation of ICN-.

In a spin: the dynamics of photoexcited ICN(-) (Ar)(0-5) are presented. Photodetachment produces quasi-thermal electron emission that leaves ICN with up to 2.85 eV of internal energy. Photodissociation at 2.5 eV leads to one-atom caging and highly solvated anion products. Calculations indicate efficient energy transfer into CN rotation upon excitation to the (2)Π(1/2) excited state. CN rotation is vital to explain the unique dynamics observed.

Dynamics of the F2 reaction with propene: the effect of methyl substitution.

The reaction of F2 + C3H6 has been investigated with the crossed molecular beam technique. The only observed primary product channel is F + C3H6F while the HF + C3H5F channel cannot be found. The reaction cross section was measured as a function of collision energy and the reaction threshold was determined to be 2.4 +/- 0.3 kcal/mol. Compared to the reaction threshold of the F2 + C2H4 reaction, the methyl substitution effectively reduces the reaction threshold by about 3 kcal/mol. The product time-of-flight spectra and angular distributions were measured and analyzed. The angular distribution displays strongly backward, indicating that the reaction is much faster than rotation. All experimental results support a rebound reaction mechanism, which agrees with the structure of the calculated transition state. The transition state geometry also suggests an early barrier; such dynamics is consistent with the observed small kinetic energy release of the products. Except for the different values of the reaction thresholds, the dynamics of the F2 + C2H4 and F2 + C3H6 reactions are remarkably similar.

Barrierless reactions between two closed-shell molecules. II. Dynamics of F2 + CH3SSCH3 reaction.

A second example of a barrierless reaction between two closed-shell molecules is reported. The reaction F(2)+CH(3)SSCH(3) has been investigated with crossed molecular beam experiments and ab initio calculations. Compared with previous results of the F(2)+CH(3)SCH(3) reaction [J. Chem. Phys. 127, 101101 (2007); J. Chem. Phys. 128, 104317 (2008)], a new product channel leading to CH(3)SF+CH(3)SF is observed to be predominant in the title reaction, whereas the anticipated HF+C(2)H(5)S(2)F channel is not found. In addition, the F+C(2)H(6)S(2)F product channel, the analog to the F+C(2)H(6)SF channel in the F(2)+CH(3)SCH(3) reaction, opens up at collision energies higher than 4.3 kcal/mol. Angular and translational energy distributions of the products are reported and collision energy dependences of the reaction cross section and product branching ratio are shown. The reaction barrier is found to be negligible (<<1 kcal/mol). Multireference ab initio calculations suggest a reaction mechanism involving a short-lived intermediate which can be formed without activation energy.

Coordinative modulation of human zinc transporter 2 gene expression through active and suppressive regulators.

Zinc transporter 2 (ZnT2) is one of the cellular factors responsible for Zn homeostasis. Upon Zn overload, ZnT2 reduces cellular Zn by transporting it into excretory vesicles. We investigated the molecular mechanism that regulates human ZnT2 (hZnT2) gene expression. Zn induces hZnT2 expression in dose- and time-dependent manners. Overexpression of metal-responsive transcription factor 1 (MTF-1) increases hZnT2 transcription, whereas depletion of MTF-1 reduces hZnT2 expression. There are five putative metal response elements (MREs) within 1kb upstream of the hZnT2 gene. A serial deletion of the hZnT2 promoter region (from 5' to 3') shows that the two MREs proximal to the gene are essential for Zn-induced promoter activity. Further mutation analysis concludes that the penultimate MRE (MREb) supports the metal-induced promoter activity. The hZnT2 promoter has also a zinc finger E-box binding homeobox (ZEB) binding element. Mutation or deletion of this ZEB binding element elevates the basal and Zn-induced hZnT2 promoter activities. Knockdown of ZEB1 mRNA enhances the hZnT2 transcript level in HEK-293 cells. In MCF-7 (ZEB-deficient) cells, expression of ZEB proteins attenuates the Zn-induced hZnT2 expression. However, expressions of MTF-1 target genes such as human ZnT1 and metallothionein IIA were not affected. Our study shows the expression of the hZnT2 gene is coordinately regulated via active and suppressive modulators.

Barrierless reactions between two closed-shell molecules. I. Dynamics of F(2)+CH(3)SCH(3) reaction.

A detailed experimental and theoretical investigation of the first-reported barrierless reaction between two closed-shell molecules [J. Chem. Phys. 127, 101101 (2007)] is presented. The translational energy and angular distributions of two product channels, HF+CH(2)SFCH(3) and F+CH(3)SFCH(3), determined at several collision energies, have been analyzed to reveal the dynamics of the studied reaction. Detailed analysis of the experimental and computational results supports the proposed reaction mechanism involving a short-lived F-F-S(CH(3))(2) intermediate, which can be formed without any activation energy. Other possible reaction mechanisms have been discriminated. The decay of the intermediate and competition between the two product channels have been discussed.

Dynamics of the F2 reaction with the simplest pi-bonding molecule.

The reaction of F(2)+C(2)H(4) has been investigated with crossed molecular beam experiments and high level ab initio calculations. For a wide range of collision energies up to 11 kcal/mol, only one reaction channel could be observed in the gas phase. The primary products of this channel were identified as F+CH(2)CH(2)F. The experimental reaction threshold of collision energy was determined to be 5.5+/-0.5 kcal/mol. The product angular distribution was found to be strongly backward, indicating that the reaction time scale is substantially shorter than rotation. The calculated transition state structure suggests an early barrier; such dynamics is consistent with the small product kinetic energy release measured in the experiment. All experimental results consistently support a rebound reaction mechanism, which is suggested by the calculation of the intrinsic reaction coordinate. This work provides a clear and unambiguous description of the reaction dynamics, which may help to answer the question why the same reaction produces totally different products in the condensed phase.

Dynamics of the F2+CH3SCH3 reaction: a molecule-molecule reaction without entrance barrier.

The F(2)+CH(3)SCH(3) reaction was studied with crossed molecular beam techniques and high level ab initio calculations. Significant reactivity was observed even at low collision energies, consistent with the negligible barrier height obtained from the ab initio calculations. All experimental findings are consistent with a weakly bound reaction intermediate of F-F-S(CH(3))(2) structure, which possesses a special type of three-center four-electron bonding. Analogous intermediates can also explain the reactions of F(2) with CH(3)SH and CH(3)SSCH(3).

Crossed molecular beam studies on the reaction dynamics of O(1D)+N2O.

The reaction of oxygen atom in its first singlet excited state with nitrous oxide was investigated under the crossed molecular beam condition. This reaction has two major product channels, NO+NO and N2+O2. The product translational energy distributions and angular distributions of both channels were determined. Using oxygen-18 isotope labeled O(1D) reactant, the newly formed NO can be distinguished from the remaining NO that was contained in the reactant N2O. Both channels have asymmetric and forward-biased angular distributions, suggesting that there is no long-lived collision complex with lifetime longer than its rotational period. The translational energy release of the N2+O2 channel (fT = 0.57) is much higher than that of the NO+NO channel (fT = 0.31). The product energy partitioning into translational, rotational, and vibrational degrees of freedom is discussed to learn more about the reaction mechanism. The branching ratio between the two product channels was estimated. The 46N2O product of the isotope exchange channel, 18O+44N2O-->16O+46N2O, was below the detection limit and therefore, the upper limit of its yield was estimated to be 0.8%.